While these checks are annoying, keep in mind (as most of you have) that it is Disney policy not that the resorts' housekeeping or managerial staff. The standard is that each room, each day should be checked and trash removed. As with any company or resort or business, sometimes communication between various elements--say, housekeeping and custodial--is lacking. That such a drop in service plays out when any guest is there certainly isn't desirable nor intended...but it is inevitable given human nature.
Take a smaller resort with, say, 120 rooms. That's over 43,000 rooms in use/available over the course of a year. Assuming a fair number of those rooms are turned over with check-ins or taken out of inventory for deep-cleaning, maintenance, etc., you're still going to have upwards of 20,000 room checks annually--a staggering amount. Expecting any group (in this case, resort CMs) to perfectly do their jobs is unreasonable. Now, that being said, if you have concerns or when problems arise, certainly contact management to smooth out the issue or reach a reasonable compromise.
Housekeepers and other CMs who do the inspections should knock three times, loudly, before entering a room with enough time in between to allow someone to get to the door by the end of the third knock and wait. They won't always do this if rushed. They should also not be just asking to take trash if you're in the room--the requirement is to have the guest step outside or tell them a time to come back later when they won't be in the room. Again, sometimes the CMs are rushed, have had a bad day, or are simply fatigued to the point of skirting guidelines. I'm not excusing them, just admitting they, too, are human. And, no, it's not a fun duty. Imagine knocking on 50+ doors on any given day. The CM hopes no one is in so that she/he can do the job quickly and efficiently. However, if only 2 in 10 are in the rooms, that's 10 people to try to get them to understand the CM is only doing a job and hoping none of those 10 will get cranky about it (small odds there).
As for the benefit, usefulness, or absurdity of the procedure? Again, that's a Disney policy so make your voice heard. Be aware, however, that dangerous items and concerns are found almost daily across the spectrum of resorts. Just because you think they're silly or you would never do something like that (or that you would hide things) doesn't mean everyone does. All of this to say, yes, it's annoying and, yes, it can be disruptive and, yes, the procedure doesn't work correctly all the time. However, in the end, there is a purpose behind the checks.