Required materials have a checklist on the applicant status portal, but often colleges do not list unrequited materials. IS the only way to check whether these materials are in the file to call the college? Should this be done?
Without knowing the college in question, yes. Or email.
It depends Personally, if I went through the time and effort of putting an extra thing together, like a supplement, I would want to ensure they received. If it were non-required Subject Test scores, where they show they have my SATs, then I would assume that all scores were received. It won’t hurt to ask “Just checking to make sure…” I’m not a big fan of bugging admissions offices about small things, but if they did not want the calls/emails, then they should have the portal show all materials sent. 
S19 sent emails to make sure his art portfolios got to schools that didn’t put them as checkmarks on their portal list. Schools got back to him right away. It wasn’t a big deal.
Yes, call or email admissions to confirm. We did a lot of that. It doesn’t hurt. If anything, it shows initiative, attention to detail, and that you care. Also, in my experience, admissions counselors are more likely to remember the students who check in with thoughtful appropriate questions. Worst case scenario, they don’t care one way or the other, so it made no difference except that you got your answer.