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FYI, I have a hallman boost controller on my car.
So, I noticed the other day that one of the little rubber nipples I capped off the stock boost controller with was missing ( the very top one). It has been like this a couple weeks I would guess, running ~11-12 psi the whole time. Now, I know that it is a good idea to have this capped off. Does anybody know any specific adverse side effects to not having it on though? Im kinda curious. Thanks!

It might be a small vac leak, no harm I can think of.

It could potentially have been a small vacuum leak, sucking unfiltered and unmetered air in. It's so small that the unmetered part is not a big deal, but in theory if there was a lot of dust around the engine could have sucked it in through there. In practice, you're probably fine even if a little dirt did get in, but I'd cap it off again right away, or maybe put a small air filter on it.