they use both. they always use as many resources as possible!
it depends on what kind of look you want to have...
I guess for Kubo Tite, it looks like they use paper, scanners, screentones, and photoshop
but for the covers, I'm not too sure, it looks like they either use the following
1) paper, scanner, photoshop
2) tablet
it's difficult to tell, tablets are used for convince wise and are really useful when you are a pro/want to be a pro and want to write manga or do art for the rest of your life.
but if your like me, a person who is too cheap to buy a tablet. a scanner, and photoshop and buying/stealing/downloading screentones is a very good start