Yes -- fish is not bash, so anything defined in your .bash_profile etc. will break, though there's usually an easy alternative way to do it in fish. Scripts should be fine though, since they usually explicitly call bash when you run them, so will still run using bash.

I switched to fish about six months ago and have been very happy with it. I spend a lot of my working day in the command line, though not doing anything exotic, and find it very pleasant to use.