Is the Java Virtual Machine reloaded by the Domino server every time a Java agent runs?
Since the agent manager process remains active after it finishes executing the agent, I wouldn't think so, but I can't say for sure.
What I do know is that the agent is reloaded every time it runs, and a new Java thread initialized. If you find that performance is a problem and you want to eliminate the overhead associated with starting up an agent, consider using a servlet instead. The following references may be helpful.