Personally I am less concerned with the usage of suffixes than I am of setting a comic in Japan without having an understanding of the culture. (I am assuming it is set in Japan?)
Adding the name suffixes will add that taste of Japanese culture and is probably what some of your audience may be looking for; those who are familiar with it, however, will be turned-off. It is pretty hard for me to read comics with Japanese characters set in Japan by people who know only the bare minimum of what school life, much less Japanese culture, is like, scraping by on things gleaned from manga.
Very few of my Japanese friends use chan with me, though some do, even when speaking English so I honestly don't find it that awkward. Plus, suffixes like chan and kun kind of denote something we can't easily say in English, so they are left intact in many translated works. As you can see, there are some strong arguments for yay or nay. You can write about whatever you want. Just take care, treat it with respect, and do your research (which is part of the reason you asked, so that's good!). If you want to do it, go for it! It is your decision in the end.
- In terms of hierarchy, it is so freaking complicated and unless you have experienced it, it is really hard to describe. Japanese Language books kind of make it seem cut and dry. It is not! I lived in Japan for three years. New homeroom teachers called all students -san, and even halfway through the semester most of the girls were still san while the boys became kun in JHS and ES (in special cases, chan, but it is very very uncommon). Only in elementary schools did I see san become chan regularly for girls. In very formal situations, all students became san again (i.e. graduation). As for what I was addressed as, usually sensei or san, sometimes nothing at all. I never used suffixes for the students though, and called my coworkers and friends by what they asked me to call them … regardless of age. One of my dance teachers, only a few years older than me, was called -chan by everyone -- even the third graders! Because of how I learned Japanese, with all that hierarchy junk, it took me a very veeerrrry long time to call him chan. Still, better to err on the side of safety and use san, I thought!
… I did live in Kyushu though, and I am told it is much more laid-back than the mainland. So yes, in the end, the suffixes can be complicated.