I always have all the mean services stopped before and after an upgrade otherwise they start messing with my drive like the new cloud with my USB passport that locks the whole system.
I don’t recall doing anything different this time around. In fact the other Cloud that was upgraded to OS 3 that had exhibited the no mount USB symptoms started to mount my USB drives with no problems. The one difference on the other one was that I did a shut down, removed from shelf, then rebooted it up on my desk. Then all my USB WD Passport, My Books (3 of them now) all mounted without a hitch.
This last one that I had downgraded even has the Public folder set to private; in fact it is still that way at the moment. Private I think.
One thing to note though, all my services that I stop, they are only temporary. They restart normally on reboot. The reason that I don’t make them permanent was the 3.04 upgrade of which I did stop the two scans permanently using
update-rc.d wdphotodbmergerd disable
update-rc.d wdmcserverd disable
That was my first scary update in which I was locked out of SSH until I did a 40 second reset of which I attributed to the permanent service removal (which wasn’t true). Nevertheless I vowed that any upgrades will be as close to stock as possible, with the services stopped during the upgrade otherwise they will overload the CPU with both scanning and upgrading at the same time.
To answer your question… yes a bunch of services were stopped during the upgrade, but not the permanent kind. Even wdnotifierd was turned off as well as wddispatcherd.