Well, there is nothing about the cut that will create a problem (unless you damage the plug while cutting it). There are a lot of miners who have been using the x1 extenders for a long time without issues. Off the top of my head, here are the issues I have read about on this forum: 1) some motherboards won't work with the x1 extenders in x16 slots (they won't recognize the cards plugged in this way). 2) Even if the board does recognize all your cards, some have reported having to reboot several times before all of their cards are recognized. 3) you want to get good cables, as some have reported burnt cables. I think one of the things you want to look for is "split" ribbon cables. For the x1 connectors, there should be two separate ribbon cables. For the x16 connectors, there should be three separate ribbon cables. This does not guarantee that the extenders will be good, but I've noticed that those reporting problems often have cables that aren't split. Keep in mind that you don't have to get the x1 --> x1 extenders and cut the female end. Instead you can get x1 --> x16 extenders, and even x16 --> x16 for the standard slots. I just ordered 2 x16 --> x16 and two x1 --> x16 from 9mart.com ($9 for a pack of two, free shipping). I'm not saying this is the best place to order from, but these should work OK. Keep in mind that they are little on the short side (12 cm). This isn't a bad thing unless you need the extra length for some reason.
Edit: If you are thinking about cutting the x1 slot on the board, I wouldn't recommend this since you are sol if you damage it. But I did read a post on another forum (forget where) where someone used a soldering iron to burn the slot so a video card could fit. Still don't recommend this, but it is probably the best way to go if you really want to modify the slot on the board. Extenders allow you to separate the cards more for better cooling, so I think they are worth it over cutting plugs on the board.