Hmm, I certainly do not want to dissuade you from leaning OOP, but, for most practical purposes, you can really use OO modules without having to know much about OOP (except for the user interface). It would be different, of course, if you wanted to expand Bioperl (say subclassing some methods, for example), in which case you would really need to understand more about the ins and outs of OOP.

Having said that, I certainly would encourage you to learn OOP if you need it. It might even help you understanding and better using Bioperl.