WIth our older single-glazed door with sidelight, we had the glass in the sidelight replaced with a single-glazed pane with a hole in it. The guy who cut the glass for us was someone whose name we pulled out of the Golden Pages. He was sceptical that it would work, but he gave it a go and it worked out fine. He needed the dimensions of the glass pane, the diameter of the hole required for the cat flap, the position of the hole relative to the bottom of the glass, and he then cut the glass before he called to the house.
When we had our windows and door replaced, we asked several companies whether they could provide a fixed double-glazed unit with the appropriate hole in it. Some of them immediately said no, one of them even started a row with me and told me to forget about a cat flap (needless to say, we didn't use his company), but the company we went with were able to do it and it has been great. Mind you, they never gave us a breakdown of the cost of making that glazed unit (it was made in the factory in Denmark where the windows were made) so we don't know how much it added to the cost. I also don't know whether they would have considered doing this unless we had been buying a full set of windows from them. Further still, if you are looking for this in a moving patio door, that may raise some issues too.
One option to consider is replacing the entire section of glass with a wooden/pvc/whatever piece, and make the hole in that. If it is a large area, maybe you could have the door adapted so that the portion that takes the catflap is partitioned off from the rest of the door so that the catflap area is non-glass and the rest is glass. Yet another option is to put the cat flap through a wall - there are flaps available that are designed for this, but you would want a reliable builder to do this for you if you are to avoid letting dampness into the house.
One other thing to bear in mind: we opted for windows with a very good U-value for a high level of insulation, but the area immediately around the catflap is one of the main places where condensation appears. It makes sense that the presence of the catflap reduces the insulation in that area, but I often wonder whether it has a bigger (negative) impact than I had anticipated (not helped by the fact that the catflap is in a door set into a north-facing wall though).