1) if you decide to run compact as a PRE_APP_QUIESCE task, be sure to increase the agent timeout by a significant value to allow enough time for all compact operations to complete. I've not run compact as a PRE_APP_QUIESCE, so I am not sure of the exact behavior.
Domino will either:
a) simply accept the command and return a zero error code immediately - this means that the compact will start but Snap Creator will continue on normally while the compact is in process. You may have a database or two locked as a result.
b) Domino will wait for the compact operation to complete and then return the zero error code. This may mean that the Snap Creator Agent is alive for a long period of time. This will increase the overall time Snap Creator runs and will necessitate a long timeout period on the agent.
2) Please pay attention to the type of compact operation you are running in Domino. Generally speaking (knowing absolutely nothing about the environment) we recommend compact -B -S XX with XX being either 10 or 15. This means that compact will only run when there is greater than XX% (10 or 15 suggested) whitespace in a database.
If you run frequent compact -c operations you will generate very large snapshot sizes. There is nothing wrong with an occasional compact -c, but you should not perform this operation very frequently. This is detailed in NetApp TR-3917: http://www.netapp.com/us/media/tr-3917.pdf
Please feel free to let me know if you have additional questions.