I got this issue as well and many times i do register user or send a transaction to the merchant account this license validation appear given around 2-3 minutes on response to finish the transaction which is very concerned.
I haven't looked at the code but they may do the same call to verify license and simply not display the notification of upgrades if that checkbox is checked....
2-3 minutes for a response is pretty long. I would think that if everyone was experiencing this type of delay (I.e. a cs-cart server issue) that people would be screaming. Even the default TCP timeout is 60 seconds. So my guess is you have something else going on which is causing your delay. Note that licenses are not checked from the customer side which is where checkout and payment capture is done.