The answrers to your question
1>Can I backup a SAN drive?
Yes as a SAN srive is seen by windows as a local disk drive you can back it up as a local drive.
2>Should I be using open file agent on my backup server?
If you have a lot of open files on the drive then you should use the open file agent.
3>What happens when there is activity on my application server?
It doesnot matter moch to backup exec if there is a lot of application on your application server the performance of backups might degrade a bit other than that nothing much to worry about.
Hope this answers your questions.