you have thousands of systems with compression on the boot drive already running EEPC? As long as you are upgrading, and not migrating (ie, not going from 5-6) it will work fine, but you will not be able to install v6 on a compressed system.
There's a function in the competitivecheck class of autodomain.vbs which will show you how to query a drive using WMI to see if it's compressed or not - you can do that across the network even.
In some cases i have read, compression is making issues while upgradation/synchronization. And even we faces the issues previously. So we dont want to take risk.
We are upgrading from 5.1.5 to 5.2.5 are you sure it will not create any issues ?
it's not supported so I can't be sure of anything - but compression is only an issue during the creation of SBFS, so as long as you don't do anything that requires a re-creation, like an eBoot, or a disable/enable, you'll be fine.
My advice would be to decompress the root dir of your boot drives - there's nothing in there that compresses anyway, and users should not be creating folders or storing data there either.