Ultimately, they will play whatever you give them. They may grumble about it, but they'll play it. The advantage of putting two or more instruments on a part is that in mid rehearsal you can say, "Flute 2, join flute 1 in mm. 67-71." It allows you to change the doublings on the fly. When I recorded my violin concerto, I had all four horns on the same part, and we moved things around in the section during the recording. Once a piece is exactly the way you know you want it, by all means, split them all out into separate parts, but if you are hearing something for the first time, it is very helpful if you have some flexibility.