$5/estate is the new $5/nothing, with Shelters in. No downside to doing that, is there?
Of course there's a downside--this is Dominion, a game composed mostly of edge cases glued together by a small handful of rules. And this is a forum dedicated to finding them!
The three big cases where a Hovel would be superior are where you would prefer a junk $1 over a junk $2, where having a card with type "Victory" would be problematic, and Cornucopia cards that care about variety. The first case is fairly easy to cover: Upgrading into a choice $2, having spare change for a Forge, leaving a target for Swindler that would net you a free Poor House, etc. The second is a bit more difficult, since most cards that care about card type would have you prefer a VP card over a card with none of the 3 core types. The only case I can think of is your opponent's attacks: I would rather turn up a Hovel than an Estate if I'm getting hit by Rabble or Jester or Bureaucrat. The third case is obvious: Fairgrounds, Menagerie, Harvest.
There's also an edge edge case, where you do want to trash your Hovel, but not on your opening hand, because there's a combo you could do later in the game. The major example would be to provoke Market Square's reaction. It's possible that you would also want a mid-game trash in order to shrink your hand size for a draw card like Watchtower or Library... since Hovel only triggers on-buy, this would require buying an alt-VP card from the Black Market deck. Theoretically possible, but in no way worth planning for.