AThe mind boggles! I don't know if your colleague is a man or a woman, although that is irrelevant. I also have to make the assumption that the magazines were pornographic. If this is the case, then there is no doubt that they should not be in school.
You should have removed them from the desk, put them in a sealed envelope and handed them to the teacher. At the same time you should have said how you came upon them and explained that you didn't want the children to see them by accident. It's a bit late for that now, however. Presumably you just shut the drawer and walked away.
You're left with one course of action; speak to your colleague, admit to rifling through their desk and make your point about pupils not seeing such publications. The teacher could, of course, have taken them from pupils and forgotten them, or have been planning to deal with the situation the next day. You won't know unless you ask.
If the magazines were the teacher's personal property, then it is no business of yours, except to insist that they do not appear in school.
There are two valuable morals to this story. First, don't go through other folks' drawers, and second, do organise yourself better. You should go out and buy yourself a little tool-box that can hold everything a busy teacher needs to have readily at hand - including her very own staple gun!