During our NS implantation a couple years ago I feel like many bundles were installed. What is the best practice to see if we are actually utilizing a bundle or if we can delete it?

A lot of it is just knowing what the bundle is meant to do. You can check scripted records and see what is deployed to each of your records...Or check the "last run date" for all your scripts, however, that isn't always the best indicator because a lot of scripts continue to run even though you technically aren't "using them"

Before deleting bundles, in addition to MG's comments, I'd verify that all the fields added by the bundle are not being used. You may be populating a field from an otherwise unused bundle without realizing it. If you delete the bundle, that field and all the data that was in it goes away and isn't recoverable. I'd be 100% sure and check extensively before removing anything. There's no undo.

@RJMNS that's a very helpful note. I was planning to do some clean-up as well. If we stop using a SuiteApp or bundle like Bill.com, Versapay, MerchantE, etc., the bundle or SuiteApp can remain installed so that we can keep our data, right?

Most bundles I've dealt with they don't force you to uninstall @Luis, but it's likely a case-by-case basis. I'd probably check with the vendor to verify.