What you're talking about are partly what's referred to as accessory lifts, and yes, they're fine as long as you don't go to the point where they weaken you for the main lifts (do them after your main lifts, and don't go crazy). They're generally focussed on improving the main lifts, but plenty here do them purely for aesthetics too. For me, it's mostly additional chest and shoulder work (can't be arsed with big arms, they're useless to me), which I do for OHP / bench improvements... he says, like he ever improves in OHP or bench.
Almost all of these programs specify when you should move on. It's common to deload three times and then change your methods or program. If you don't know what a deload is, you haven't read enough on the programs.
Edit - Oh, and you wont be decreasing the weights you've been using for your upper body work on the whole, because almost none of the beginner programs specify those particular lifts anyway.