I'd imagine that suspending probably causes the PSP to do something with the "protected" area of memory that the loader is running in by re-initialising the UMD interface and causing it to un-hook the patches. Until they implement a separate hook to bypass that process as well, suspend mode won't work. (Assuming it can be done at all).
I'm impressed with how well suspend works. I left THUG2 running overnight and forgot about it, picked it up the following day and continued playing. Suspend mode seems to be pretty friendly with the battery as well as it hadn't used much of it.
I think Hook-boot does more low-down & dirty patching than Fastloader does which might be why it works "differently" (not always better) than things. With the sourcecode for both applications now available, I'd say someone (Humma or the Hookboot coder(s), or a 3rd party) may well amalgamate things and make a "super"-loader