When placing a new cpu cooler, should I take out the mobo to check if the push pins locked in? Isnt it good enough if its securely seated and I hear the clicks? I just dont want to damage anything, and avoid the hassle
yes it's perfectly fine to not take it out if it is clicking into place. This place from where i get most of my components actually lay the case on one side and install a replacement cooler almost every time.
It should be fine. But do clean your cpu's remaining thermal compound from older cooler.