I've been feeding this mother cat because she had 2 kittens for about 3 days. I checked this morning and she and the kittens aren't there anymore. Why did she leave and will she ever come back?
Mother cats will move their kittens if there is danger or possible danger. It is fairly common and often isn't a major indication for worry. It could have been as simple as a dog got too close or car backfired. If you've been feeding her regularly she likely will continue to swing by for food and will probably bring the kittens around once they are mobile.
The best thing you can do for this little family is get them spayed/neutered. I'd recommend trying to contact local resuces about feral TNR programs that could help trap mom and find homes for her babies.