I haven’t yet seen a program-update-available popup since upgrading to 6 (which makes sense, although I imagine I should be seeing something for that new pre-release any time now). But back in the “old days” (5.1? 5.0? 4.8?), if you used the default “ask” setting for program updates, the popup did not stay up awaiting your action.
Keep in mind you always have that “show last popup” available (in the tooltray-icon menu) … don’t know if it’s still the case in v.6, but the “update now” link in that used to work just as if you were looking at the original popup.