I don't think there can be any doubt about the pom poms and my hunch is that the quad 0.5"s would not have been replaced.
The question is whether any Oerlikons were ever fitted, shortly before Exeter was sunk, in the bins for them fitted during the 1940-41 Plymouth rebuild (from which she emerged with no Oerlikons).
For part of an answer to this question please see my post of 24 Oct 2007 here http://www.shipmodels.info/mws_forum/viewtopic.php?f=48&t=10618&start=200
As you may be aware, Kevin Denlay dived Exeter well before her wreck was removed by illegal salvors recently.
You mention images showing 20mm in situ in the bins on B & X turret. I would be very interested to see these. There are of course numerous photos clearly showing no 20mm in these tubs from March 1941 up until about February 1942, but then a degree of ambiguity in what can be seen there arguably creeps into the few images of Exeter in her final days.