they built the fence on land, the sub is in the sea. the fence as far as i am aware doesnt even cut off where the pier is, they built it further in shore. so he can get to the sub and he can cross water and go inside water in john locke's form, but not as the smoke monster.
Yes he can but he'd have to have a decent sized army to take all of them out, plus i dont think the writers want to oust Widmore and crew yet.