Easy enough to test, so I did...

I just created a VAN with a $10 limit. I then went to Comcast and paid $3 off my bill using that VAN. It was approved, and immediately showed up as a Pending transaction on both my credit card and on the VAN.

I then Deactivated the VAN, waited about a minute, and attempted a 2nd payment using the same card, this time for $4. The payment was declined with the reason :
Card Processor Decline (DO NOT HONOR)

Neither the VAN or my main CC transaction list show any mention of the $4 transaction. My presumption is that the $3 charge will go through without issue (as it's already approved and pending), but the $4 one attempted after the card was deactivated clearly won't.

So yes, deactivating a VAN does stop any future charges - but almost certainly won't stop any that are already pre-authorized (and nor should it!).