I always figured Deanna Troi was named in honor of Helen of Troy, the archetype of great beauty (like "Elaan of Troyius" before her). I wouldn't be surprised if Donna Troy was named for the same reason. So it would be a case of both names being independently influenced by the same thing, rather than one being based directly on the other.
And yes, the characters happen to resemble each other, but that wasn't planned. Remember, they were originally considering Denise Crosby for Troi and Marina Sirtis for the security chief, but finally decided to switch them. So it's not like they were specifically intending Troi to be a long-haired brunette.
TNG was created by Gene Roddenberry, David Gerrold, D. C. Fontana, and Bob Justman (although Roddenberry hogged all the screen credit). I'm not aware of any of those four being comic-book fans. And Donna Troy/Wonder Girl is a pretty obscure character outside of comics. Her only film or television appearances were in three episodes of a 1967 Saturday morning cartoon, and I'd be surprised if they used her real name there rather than just calling her Wonder Girl.
It's also worth noting that TV producers generally try to avoid naming their characters too similarly to other fictional characters or prominent real people, for fear of legal complications. Thus, I'd say that as a general rule, if two fictional characters have similar names, that actually suggests that the creators of the later character didn't know about the earlier one.