Bumps stops are on each strut rod to prevent metal to metal contact, kinda like a little absorber. If it were to hit metal to metal then suspension parts would get bent & possibly an injury to a passenger inside the vehicle. The reason they should be cut(shorter) is with lowering springs & "stock"length struts you are greatly reducing the amount of suspension travel & bump stops take up some of that room. Your basically cutting them to increase suspension travel lost by lowering.
By "stock" length struts I'm talking about obviously stock, KYB, Tockico. I don't recommend any more than 2" drop with "stock" length struts. There are always Koni yellows or by that point you should really be investing in a true coilover, not some crappy sleeves.

As you can see, if there were un-cut bump stops there would be minimal travel with often bottoming out. That image is an extreme case of lowering, but you get the idea.