What version of SQL? If MS, the SQL server sometimes has limitations on how much it will provide at one time. AD queries can cause this problem as well.
I don't believe there is a limitation with the SQL configuration - will check up on this though. It works fine when viewing many thousands of endpoints in the system tree, however doesn't respond the same way when using ePO web-API, which to me feels like a config issue with web-API (eg some sort of throttling), or some sort of bug with web-API. Still waiting on a response from support about this.
Solution: this was a syntax issue. Got the answer from Intel Security support. Here is the correct syntax to use when querying large amounts of endpoints in a system tree. Note: this is purely using webAPI, not relying on someone's powershell module such as "ePowershell" or similar.
Incorrect syntax I was trying: curl -k -u username:password "https://eposerver:8443/remote/epogroup.findSystems?groupid=1&searchSubgroups=tru e"
Correct syntax provided by Intel Security support: curl -k -u username:password "https://eposerver:8443/remote/epogroup.findSystems?groupid=1&searchSubgroups=tru e&:output=terse"
The extra bit on the end "&:output=terse" was what made the difference, and allowed the query to complete in a minute or 3, rather than 3 or more HOURS.