Check out replay 1981426 (Sandbox test:1981792). I start T3 upgrade, pause it, and then build storage around the mexes with queued assist orders after. My mexes continue to produce only 6 mass instead of 9 when storage are built around them, until I actually start the upgrade to T3 with the engineers.
Further investigation in a sandbox test with no sim mods whatsoever reveals that a mex that is upgrading at the time that adjacent storage is constructed will never gain the bonus from that storage, whether the upgrade is paused or not. A mex that was not upgrading at the time gained income as expected.