This is long. For that I apologize but the issue is somewhat complex.
Title III of the ADA prohibits discrimination against any individual with a disability by "public accommodations." This includes theme parks. Certainly, an individual who has no arms has a disability.
Under Title III, “discrimination includes . . . a failure to make reasonable modifications in policies, practices, or procedures, when such modifications are necessary to afford such goods, services, facilities, privileges, advantages, or accommodations to individuals with disabilities . . . .” 42 U.S.C. § 12182(b)(2)(A)(ii) (emphasis added).
The Supreme Court explained the meaning of this provision in Spector v. Norwegian Cruise Line Ltd., 545 U.S. 119, 129 (2005):
Eligibility criteria that screen out disabled individuals are permitted when "necessary for the provision" of the services or facilities being offered, §§ 12182(b)(2)(A)(i), 12184(b)(1). Policies, practices, and procedures need not be modified, and auxiliary aids need not be provided, if doing so would "fundamentally alter" the services or accommodations being offered. §§ 12182(b)(2)(A)(ii)-(iii). Auxiliary aids are also unnecessary when they would "result in an undue burden," § 12182(b)(2)(A)(iii). As we have noted, moreover, the barrier removal and alternative access requirements do not apply when these requirements are not "readily achievable," §§ 12182(b)(2)(A)(iv)-(v). Additionally, Title III does not impose nondiscrimination or accommodation requirements if, as a result, disabled individuals would pose "a significant risk to the health or safety of others that cannot be eliminated by a modification of policies, practices, or procedures or by the provision of auxiliary aids or services," § 12182(b)(3).
Notice that the statute provides it is not discrimination if there is a "significant risk to the health or safety of others." Similar language appears in Title I of the ADA (which governs employment). The provision governing employers states that employers may have a policy which requires employees "not pose a direct threat to the health or safety of other individuals in the workplace." The EEOC interpreted this language to permit employers to have policies which prevent employees from performing tasks that would pose a direct threat to the employee (not just others) and in 2002, the Supreme Court upheld that regulation. Chevron U.S.A. Inc. v. Echazabel, 536 U.S. 73 (2002). The Department of Justice interprets Title III, however, and its regulations do not include a threat to self provision.
Oddly, and this is important, I can find no decision saying that public accommodations (remember, this includes theme parks) can exclude individuals from activities because the activity poses a risk of harm to that individual. At least one district court decision in California has held a public accommodation (a Marriott resort golf course) could not defend an ADA claim on the ground that the requested accommodation would pose too great a risk of harm to the individual. This is the same standard Disney relied upon to ban Segway use in theme parks. Notably, Disney did not argue Segway use posed a risk to the user, it argued the use posed a risk to other guests.
If this interpretation of Title III is correct, the question is how does permitting someone without arms to ride the attractions pose a significant risk to the health or safety of others. (This focus, by the way, shows why getting a waiver wouldn't be helpful. A waiver would only protect Universal if the individual sued. It would not protect Universal if others sued Universal because they were injured because Universal let a disabled individual ride the attraction.)
Universal is not the only theme park to implement a policy of this nature (nor is it the only one to be sued for having this kind of policy). Six Flags changed its policies because in 2011, a military veteran and double-amputee died after being ejected from a roller coaster (not at a Six Flags theme park). An inspector concluded that the veteran's height and lack of lower limbs to brace himself caused the ejection. At least two ADA claims have been filed because of this policy. One decision, from Texas, refused to dismiss a teen's ADA lawsuit because the direct threat defense "cannot apply if the public accommodation can make reasonable modifications for the individual" and Six Flags did not argue it could not make an alternative design.
Bench v. Six Flags Over Tex., Inc., No. 3:13-CV-705-P, 2014 U.S. Dist. LEXIS 179313, at *14 (N.D. Tex. July 3, 2014).
In New Jersey, at Six Flags Great America, Six Flags argued that prosthetic limbs had the potential to become projectiles if allowed on certain rides. The court didn't rule on this as an objection because, as in the case at Universal, the guest wanted to ride without any prosthetic limbs.
Masci v. Six Flags Theme Park, Inc., Civil Action No. 12-6585, 2014 U.S. Dist. LEXIS 178666, at *34-35 (D.N.J. Dec. 31, 2014).
Both decisions refused to dismiss the lawsuit, holding that there were too many facts in dispute over the whether the policy was based on legitimate safety concerns.
There are two other wrinkles. The Universal "case" has not been filed in court. It is simply a complaint lodged with the Florida Commission on Civil Rights. (This is the same state agency which has ruled against Disney on ADA questions only to have a federal court rule for Disney on the same issue.
http://www.disboards.com/threads/disney-faulted-in-disability-access-complaints.3388566/ and
http://www.wdwinfo.com/news-stories/federal-court-rules-for-disney-in-lead-dasautism-lawsuit/) I know I have written on this question before but I can't find the post or blog. I recall questioning whether the statutes gave the Florida Commission authority of over claims of this nature (they clearly think they do). in any event, Florida Commission decisions are not binding on Universal (any more than they were binding on Disney). The ADA would have permitted the woman to file suit in court without going to the Florida Commission. if I remember right, the only advantage to first filing with the Florida Commission is that it might permit her to seek damages (something she cannot get under the ADA) if she were later to file a lawsuit alleging an ADA violation and a violation of Florida's disability discrimination law.
The other wrinkle concerns Universal's liability should the disabled guest cause another guest to be injured. If, in fact, the ADA required Universal to permit disabled guests to ride the attractions, Universal could not be successfully sued under state law (which permits personal injury lawsuits) because it had to comply with the ADA. But lawsuits are never this simple. Universal could be sued for not having in place procedures or ride modifications which permitted disabled individuals from riding the attractions in a safe manner. So, if a relatedly simple and cheap "fix" would significantly decrease the risk of harm, then state personal injury laws would let someone who was injured sue Universal despite the fact that Universal had to comply with the ADA.