The Go card is only a good value if you use it for SeaWorld and
Legoland because they have the most expensive individual admission prices.
San Diego Zoo is currently $46/36 adult/child
Maritime Museum is $16/8 adult/child
Unless you can get a Go card for under $60 it won't save you for just those 2 combined.
I suggest buying tickets separately and using
AAA, Costco, or military discount if you have it. You can also find coupon deals ($4-$5 off) for the zoo - look online or in hotel brochures.