Yeah, it has hardware acceleration, but I still don't think it'd be enough to do a direct port.
Mainly the CPU... running the amount of LUA scripts that Aq does on < 1ghz wouldn't be pretty.
Aquaria also has a ton of large textures, more-so than Quake3 would... and there's only 128mb RAM. (I'm guessing part of it is used as video memory)
If I ever get an iPod Touch, it'd be a fun thing to try though. (provided someone ports SDL over)