I prefer filling out every slot.

I really like keeping the rule of 2 units per department since a lot of units are hard for me to manage. I do sometimes miss filling out every slot because it would make X meltdowns easier to do, but I decided to abandon it because it would cost me a lot of runs due to stats being spread out thin from managing so many units. Both have their own net benefit though and it's up to the player to work with whatever department setup they have.

i put 1 employ in each department

I keep a full house. I love a good block party.

I haven't been playing long but I was wondering: Would it be worth it in the long run to have a full department early on so they can build up their department loyalty bonus earlier even if you're not training them right away? Or is it just not worth the headache of trying to keep them safe?

If you have abnormalities that have high chance of escaping or killing your agents, then you may be wasting lob points to fill up the departments.

I prefer 1 agent per abno (not including tools), which I cycle around as agents level up. Usually 2-3 per department unless I'm struggling

I prefer 4 for each department. expensive, but worth having 1 of each damage type in a department.

I usually throw a lot of LOB at upgrading units, so I only have enough to afford about 3 per department, along with a few spares for when the next department opens up. That generally works pretty well, though its not a bad idea to have a lot of chumps around for the hardest day in the game, given its mechanics.

usually 3 or 4 per for me.

I only do 2 to 3