Would covering a book or module in clear plastic drop its relative value or...would covering it in plastic to keep the pristine state of the cover actually increase its value as time goes by?

It decreases the value of a book.  And, the more valuable the book, the greater the % harm to the value.  In other words, the more collectible it is, the more it harms value.

Hmm, I have a first edition DMG that meets all the criteria for a first. I bought this on ebay for a very good price- that particular tome is covered in sticky back plastic.
On the other side of the coin, I did sell "Horror on the Hill" that I had stated to be covered in the stuff and that went for far more than I'd expected.