Iirc, across all competing strategies I've tried Shelters make a Rebuild strategy perform between 0.5 and 2.5% worse. I've yet to find a strategy that loses to Rebuild on an Estate board but wins with Shelters. I'm sure that I can construct some kingdoms where it happens, but they are so rare and our ability to estimate such small discrepancies is so faulty that in practice the presence of Shelters is just negligible.
One thing to note and something quite a lot of people do wrong is that you don't want to buy a lot of Estates in a Shelters game. Before the very late stage you only want the absolute minimum number of (OV)Estates that give you an acceptable probability of not having dead Rebuilds. Loosely speaking, you want to maximize the expectation of your Rebuild plays, which is done by Rebuilding, over the course of the game, Duchy -> Province as much as possible. OVE requires already 2 Rebuild plays to get it to be a Duchy, so I usually buy just 1 Estate in addition to that. Unless there are 3+ Duchies left and you have 0 Estates or there are 4+ left and you have 1, I would be very weary of buying another Estate, it's generally better to get Silvers and buy Duchies directly.