running a free server on aternos, so ofcourse it is not a performant server in the first place, however i think there could be some improvements to make?

[WARN] [Essentials] Permissions lag notice with (SuperpermsHandler). Response took 28.091630ms. Summary: Getting group for -user-

When i install vault it complains about prefixes in a similar fashion as well.

Using minecraft 1.14.3 latest release of spigot and luckperms and essentialsx. Was using separated flat files first but then switched to a single h2 file to try to reduce the lag.

My question is are these queries cached? Is it essentials or luckperms lagging?

It is most likely the server itself lagging.
Like you just said....

running a free server on aternos, so ofcourse it is not a performant server in the first place, [...]

The only time LP reads from the disk is when a player joins or when /lp sync is run.
Meaning that if you’re running an up to date version of LP, then it means that the server itself is lagging severely.