Does being "busted" by Customs (i.e. carrying some items that should be declared, but going, and being pulled of from "Nothing to declare" lane) affects admission to the US at all?
I was let go with just a warning for my "offense", but still the customs officer took my passport and make some note in the system. Should I expect secondary inspection next time I cross the border?
Yes, you probably will be pulled into secondary again but you should be able to get this cleared up in connection with future travel by filing a "complaint" with DHSTRIP. But you should only submit a complaint if and when it happens again; you shouldn't submit one preemptively now.
I was let go with just a warning for my "offense", but still the customs officer took my passport and make some note in the system. Should I expect secondary inspection next time I cross the border?