Welcome to the forum!
Usually kittens need to be dewormed at least once when you first get them. After that, it depends on whether they are indoors or not. I would do a yearly physical with a fecal anyway. But please do not use any pet store or over the counter flea or deworming product. They can be quite dangrous for cats and in some cases deadly.
My cats are microchipped even though they don't go out. If you're going to use a collar I would definitely get the breakaway kind. They should generally fit snuggly but not too tight (obviously with a kitten you should check it regularly to make sure it doesn't get too tight as they grow). Rule of thumb is you should be able to put a finger or two through the collar.
Personally I don't like covered boxes because I don't want them breathing in so much dust. But that's just me. If you use one I would make extra sure you use a low dust litter.
As far as keeping your kitty indoors, I don't think it's cruel at all. In fact, from what you discribe of your neighbourhood, it would be the responsible thing to do. As Heather said, just give him lots of toys and a nice spot in the window and he/she will be just fine.
Also, I would keep in mind that kittens have TONS of energy so, if you decide to get one be prepared. They need a lot of time, attention and patience. If you don't think you have that I would consider an older cat.
Ask as many questions as you want! We're all happy to give whatever info we can and it's great that you're trying to find out all you can before you get him/her.
Best of luck with your new kitty!!