Aquatic is safe to visit alone during the day. Yes, there are gentlemen seeking the casual comfort of other gentlemen in the bushes on the south side of the park. As a local, I can tell you that it's pretty easy to ignore.
The bigger issue with the course is the pedestrian path that runs through the middle of many fairways. If you're there during a weekday it shouldn't be too bad, however. Bring a couple of discs you don't mind losing into the water - there are several shots where the best line to the pin requires you to aim out over the marina. If you're walking over to the park from Emeryville, you should know that the south side of the park(closest to Emeryville) is where the back 9 starts. Hole 1 is at the far northern end of the park, right near the parking lot on that side.
Go to www.ebdgc.org
to download/print a course map before you go, the course is not easy to follow for a first timer without a map.
Golden Gate is a better disc golf course in most respects- I would definitely recommend that you try to get across the bay and check it out. I know that there are transbay buses, but I have never taken one.
I would be happy to answer any other specific questions you have about the two courses.