Is it more dangerous when 51% attack happens than just having a pool with >50% hashrate?
One can't say what's more or less dangerous for a cryptocurrency value. You don't have a control group. You would need a parallel universe where Flypool had no more than 51% to compare prices there to prices in our universe.

Saying that, being decentralized it's the very point of a cryptocurrency, and very few people will invest in one of them that's actually centralized. I can only speculate what's in their minds, but maybe people invest in ZCash today hoping it will become less centralized in the future. Flypool, despite having more than 50% hashpower, like you said, probably don't mine only on their own blocks because they would make people sure the thing it's centralized. Or maybe because they sincerely want the security of ZCash against a double-spend, so the accept the smaller pools help. Both things must probably increase an overall reputation of the ZCash in people's mind and must probably keep the price a little high.