Hey ispire
I have three servers I can compare numbers with you on. One has 800 agents, our internal 6.3 system. The others have 7k and 20k agents on them. The big one can be sluggish at times but is perfectly usable.
Like you we have them split and you're right saying that the main App server doesn't need to big a beast to run on, we have them on pretty basic Hyper-V boxes. The SQL box however needs some looking at. What do you have in the way of disks? Have you split up the SQL databases, ksubscribers, temp and transaction onto their own partitions? And when I say disks throw as many disks as you can at the SQL box, trust me you'll not regret it. We run two SQL instances on the same server.
We don't use any of the Kaseya bolt-ons, And have no reason to think that's going to change any time soon. I read the comments on this community and that's enough to put me off.
We do however run some dashboards off the same SQL box and the screen shot below gives some idea of the CPU time on those. None of my Current High CPU entries are below the 1 million mark and our SQL server runs for most of the day at around the 40% mark.
Sounds to me like you need a high level Kaseya tech to have a loom at your system and see if they can pinpoint any issues. Though good luck getting hold of one of them.
Your KES stuff does seem to be running very frequently though I can't compare as we don't use.
Good luck getting things speeded up.