less travel = bumpy ride. The purpose of the bump stops is to keep the shock / strut from bottoming out (which generally will destroy it). When you lower it, you decrease your strut travel. Think of it this way: Ever ridden in a go cart? That is literally 0 suspension travel (except for some tire flex). Bumpy, right? Ever ridden in a stock benz E class? Tons of suspension travel. Smooth as butter (of course this is really over simplifying things, but you get the idea).
Most lowering springs do not have high enough spring rates to keep the car off of the stock bump stops during hard cornering. B/c of that, w/ a long (stock) bumpstop, you'll basically be riding on the bumpstop, not letting the suspension do its job. This not only makes for a harsh ride, but can also make for some skittish handling when your spring rate suddenly goes from 150# to approaching infinity (for the record: exageration) as you hit the bump stop.
I hope that helped, as I'm @ work, and it's probably pretty convoluted.