Thanks for sharing your thoughts. Glad to hear that you're enjoying the game! I'll try to answer the direct questions and cover anything that is already in the game.
The core incentive to continue playing is whether or not you find that fun for its own sake. I've made and positioned Hive Time as a play-as-long-as-you're-having-fun type game in the vein of 1989's SimCity. I am wary of making the game more attractive to people who aren't finding the experience of playing intrinsically rewarding, since this will invariably lead toward experiences that are more negative than just not finding the mid to late game interesting. I have done some early design work on a goal tracking interface and loadable scenarios as part of a possible future update, but they'd be framed around inviting players to explore and discover creating their own goals/ways of playing rather than shifting the mid to late game's focus on to gameplay-extrinsic rewards (Beepedia entry unlocking is probably the closest the game gets to that).
Regarding bee efficiency and bees taking breaks (referred to as "bumbling" in-game), that already happens, though there is intentionally no specific cell type dedicated to or required for that. The Activity screen accessible from the upgraded Throne Room shows the ratio of idle bees to working bees over time for each role, and can be used to track that once playing at a scale where this can no longer be observed for a reasonable portion of the hive when zoomed in.
The Upgraded Workshop has a cell list that can be useful for seeing the number of given cell types (such as exits) and when viewed with the "three bees per cell" rule in mind, can give an idea of infrastructure load/redundancy.
I'm wary of doing anything that specifically guides players toward highly optimised play - one of the concepts that Hive Time is built around is that too much optimisation creates opportunities for risk and instability. There are efficiency cues and a little feedback there for players who want to pursue that sort of thing (and it can be fun), but I'm not sure that explicit framing would be a good fit for Hive Time's identity (this is why the Activity screen has the name it has, while it's is called "EfficiencyMenu" internally).
I'm not intending to make relative cell position more important - making layout primarily cosmetic was an intentional design choice aimed at simplifying the simulation and giving players freedom to make hives that look and feel interesting to them without having to work against the game. As a self-embraced constraint, designing layouts where storage needs to be near exits and production facilities is wonderful, but I don't want to impose these things beyond the adjacency requirements/bonuses that some cell types have. "Triple letter score" tiles have been on my todo list since the original jam prototype, but have been lower priority than all other development.
When we spoke last night, I think you mentioned that you were running an older version and needed to upgrade. I fixed some memory leaks recently - could you send me a copy of your game log when run with --verbose if you still continue to see the object leaks warning with a current build of the game?