When you store things in OCD, they are added to any matching slots first, going down the list. So after an OCD upgrade, you have unused space in every slot. This extra space is not shown as a number, but it is there. The next time you store the same thing, those slots will be “topped up” before any new empty slots are used.
ocd:sort does not combine slots, only rearrange them. So if you want to fill those slots to the max, you must (take out stuff) and put more stuff in, yes.
The extra slots do not show on HWS Connect until they are used, but they are there.