This was the subject of one of the recent chats. I can't get to the links at the moment but they are here in this forum very recently, search for "preferential shuffling." Yes, the house can (and does) choose a shuffle they feel gives them the greatest edge. Yes, the shuffle can affect the effectiveness of your play, and some shuffles can outright defeat counting. Since that chat I've been paying attention to the shuffles used around here and a couple of the worst ones are in use here, a subject I was wholly unaware of before that (and I think it partly explains why it was so hard to win there).
Pay attention to when the dealer shuffles differently than normal. What just happened in that shoe? We think they're just passing out the cards and comparing their total to the players. Turns out alot of the dealers are doing alot more than that and following house instructions on how the shoes should be paying out, and shuffling accordingly. One of the most common changeups I have seen is that when a shoe absolutely massacres the players, they'll shuffle differently than they did the last N shoes. They wouldn't do that without a reason. Shuffling is muscle memory, you only change it when you have a reason to.
Sims would show that over the "long term", bad shoes don't matter as they get balanced by good ones and the long term behavior would be that you played as though all shoes were perfectly shuffled. While I don't doubt that's true, I would say that the presence of bad shoes certainly extends how "long" the "long term" ends up being, as it's just an arbitrary point at which you get within an arbitrarily defined margin around your EV limit anyway.
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