First yes do exclude Altiris processes (entire folder) from SEP
Second I have split (recommend this so it is not all one big inventory job ) my inventory into three different inventory runs that I do run only once a week.
1. Hardware (should be able to run this daily without issue, but do you need daily hardware inv) Full once a month and delta the other weeks.
2. Software (should be able to run this daily without issue) Full once a month and delta the other weeks.
3. File Detail (this is the one that takes the longest to complete, try to exclude as much as you can which you don't need to inventory) Full once a month and delta the other weeks.
If you have anything specific you need inventoried more often than once a week I suggest you create a custom inventory and only inventory that one thing. FD inv you would deselect all drives from being inventoried and then only include the single folders you want inventoried also in the File type eliminate all types you don't care about.
After this what kind of machines do you run? We run the main inventories ever night at 6PM and when the machine is not available it will run it the next time it becomes available. I have yet to ever get a complaint.
We do have pretty new machines though Optiplex 780's and above. I will also say though if I forced a daily full inv then I probably would also get complaints as it would be more noticable.
On my servers I do a daily inv but I'm very specific and only monitor what I want which is hardware (drive space only) and FD we monitor only the SEP DAT locations and then report on this to make sure they are not getting out of control. Of course there is a file detail inventory issue that is supposed to be fixed in SP2 where it does not always clean up the old FD records that have been deleted.
Good Luck