Will you see a 1%, 5%, 10%, x% improvement with alignment? If you are able to isolate some of the spindles of the SAN, and perform a test when it won't impact mission critical services, it is always best to test and see.
Unfortunately, few administrators have the luxury of planning for, or hearing about alignment before the storage has partitions. To backup, wipe, recreate partitions with diskpar(t), and then restore is...painful.
So I personally recommend you test and see. If the performance win is x% more IOs, then you will be in a more informed position to decide whether it is then worth the effort to align all of your partitions. On new storage, without a doubt, ALIGN YOUR STORAGE.
A _great_ tool that Exchange has made, Jetstress, makes it very easy, and quick to see how many IO's your database LUNs can sustain. Run Jetstress on a database LUN, delete the partition, align it, then rerun the test with a backup of that database on the now
aligned partition. It should take less than 5hrs to run both tests.
Jetstress: http://www.microsoft.com/downloads/details.aspx?familyid=94b9810b-670e-433a-b5ef-b47054595e9c&displaylang=en
http://www.microsoft.com/downloads/details.aspx?familyid=94b9810b-670e-433a-b5ef-b47054595e9c&displaylang=en