That might be why Baron has its Estate-gaining power in the first place. I always thought that was weird. Once in a huge while, you can pick up an extra Estate on the last shuffle that way, but it's soooo unusual -- because if you haven't gotten rid of your Baron by that point anyway, there's a good chance that +1 Buy, +$4 will enable you to buy that same Estate anyhow.
Anyway, if Shelters are the reason Baron can gain Estates, I would indeed expect Baron to be weak with Shelters, but at least they wouldn't be as bad as if you had to buy the Estates separately.