I don't think it's just a long term effect. I've already experienced this attitude from potential customers:

"So what happens when you guys get aquired and shut this product down"

"We don't plan to, it makes money and we're growing"

"If you keep growing one of the big players will get worried or interested or both and make you an offer you'd have to be stupid not to take"

It makes sense, the aqui-hire doesn't just get you a proven team with known talent, it removes a potential competitor that might disrupt the status quo. There's a reason it's happening so often and it's because it's great business.

But as a trend it's certainly going to make it harder to get customers for startups that aren't based on creating a fad-ish service for consumers but are providing services people consider important.