They live on estuary shores mostly.
The current from your filter should be just fine. Adding a wave maker might stress them out, especially stressing any fish you put in the water portion.
In 6 inches of water you're not going to fit a whole lot, even a dragon goby - perhaps a knight goby, but they'll be really skiddish.
In a 50 gallon you've got more than enough room to have at least almost a foot of water or 10" and still have plenty of head room or plant room for dry land.