Bananas are a bad example of this. They don't follow the ordinary selection processes during domestication - the ones we commonly consume are hybridized cultivars with triploid genetics; they're infertile. They reproduce asexually, so all bananas belonging to the same cultivar are clones of each other.

More generally, yes, over time you are going to get more of what you're selecting for. Which may or may not be flesh:seed ratio.