There was no special behavior for sets in Omeka S 2.0.0, but you’re probably just describing a situation where you’d used a set to set up the item pools for sites.
Omeka S 3.0.0 made some significant changes to how items get assigned to sites. Previous versions basically did a live “search” every time items were requested, so you set up the pool and things would automatically appear in a site as long as they matched the pool’s settings. 3.0.0 instead stores specifically which items go into which sites, so this doesn’t need to be recalculated every time a site is browsed or searched.
In 3.0.0 and up, the add/edit item form offers direct control of what sites a new item is assigned to. Users that were using a set per site just to assign the items to the right sites in prior versions can instead just select the desired site(s) directly. In making this change, we worked to provide features to accommodate users’ existing workflows. For users previously using the “blank” default pool setting that made a site contain all items, there’s a setting on the site that will add all new items to it by default. And as you mentioned, there’s a new setting for users to set the sites that items they add will appear in by default also.
Finally, the prior “pool” setting under the Resources section for a site can still be used to bulk-assign anything matching a search query (including selecting just all the items in a given set or sets). This isn’t automatic as it was before, but depending on the workflow could be a simple substitute (updating the assigned items just once when the site’s items are completely added, or periodically re-running it to pick up new batches).
This is a brand new change still for Omeka S, and we’re definitely interested to hear about workflows that we could be providing better support for. So if you feel that none of the new alternatives I mentioned really works for you as well as the previous system did, we are absolutely open to that kind of feedback.