It's not altogether clear what you're asking. I assume when you say you're archiving every night that you're backing up your lotus notes server using the TSM baclient's archive functionality? I'm not sure why you'd choose to do that over simply doing an incremental backup of your notes server.
In either case, the baclient will backup a file that isn't open but will not backup a file that is open by some program. This is the default behavior unless you change it (i.e. you CAN make it backup open files if you like but thats not the best idea since your file may be inconsistent). Actually it tries 4 times to backup an open file and if it's still open after the 4th attempt, it gives up and goes to the next file (you can change this as well). In the case of lotus notes, you're talking about many many database files (nsf files) which may or may not be open at the time you do the backup.
So while there is nothing wrong with archiving over incremental backups, there are some pros/cons. Retention is slightly different. The way you restore the data is slightly different. One thing i'd point out is when you archive, it always backups up a file even if that file has been backed up before aleady. With incremental, it won't backup the file a second time if it's already been backed up as it doesn't need to. I'm not going to go into the differences between archiving and incrementals here though - you should read up on the topic as there are plenty of guides available to do so.
Keep in mind though that if you are not halting your lotus notes server before running your archive or backup, you may not be backing up all your database files. Thats why they sell a data protection agent.. so you don't have to halt your server to get a complete backup of it. And also you'll be able to do incremental transaction log backups of your notes server.