Backup Exec 9.1 won't have been tested wiith 2003 R2 as R2 was release dwhen Backup Exec 9.1 was no ,longer the current Backup Exec version. It is possible that it will install and run - however any problems with stability and/or restoration of anything more advanced than the file system will be your own responsibility.
If you do upgrade to BE 2010 read the software compatibility list carefully as some early Operating System (i.e. NT4) and database technologies (early versions of SQL, Exchange etc) are no longer supported so you may have something else in yoru environment that is compatible with 9.1 but not 2010