Will fish populate artificial underground canal?
- Yes, water creatures can swim from natural rivers into any connected bodies of water including those dug out by your dwarves.
- I believe bars, grates and fortifications all let water flow but keep creatures out, including vermin at present*. The idea for allowing vermin/small creatures to pass through bars (but not grates) has been floated in the past, but to my knowledge this has never been implemented.
Also note this bug: dwarves and creatures can sometimes be pushed through grates/bars/fortifications by water flow, though in my experience this is pretty rare.
*EDIT: @Daenthy correctly notes that vermin can spawn spontaneously in habitats that support them, so vermin may still turn up in your "secure" water sources.
Vermin appear randomly in any tile that can support them. There's no way to prevent it.
As of DF 0.40.23 I'm getting salmons in a channel that is fed from a river through a grate. I cannot set up a fishing zone near the channel (don't know if it's a bug or a feature) but the salmons are definitely there.