As you are aware, aesthetics and legibility are better with the pad print. Usually worth the extra ten cents.
Molded in lettering graphics can convey the ownership of the tooling and tell savvy users that you are not buying off the shelf product and just printing it, but that is usually best in combination with a pad print in another area.
A pad print costs that little bit more, but the consumer sees that he or she gets that little bit more as well.
Molding in is usually fine for low accessed ports. If you do them in conjunction with a texture break the visibility is usually fine. Plus these days it’s hard for someone to say “IS THIS A USB PORT?” - it’s all pretty ubiquitous.
In that case I would almost side with molding them in. The added value of the pad print probably will go un-noticed, add cost, and also has lower reliability (can be worn off easier if the surface gets rubbed or scraped over time).