Ideally, we would want to defer optimizing until the outside of business hours, including related alerts. Since this process slows down the machine, and the notifications distract the users. It is for our purposes decidedly non-essential to business day operations.
I have confirmed with Apple that this dialog is not currently suppressible, by design. In reality, these optimization cycles are required after upgrades and are not optional, and thus, you cannot delay them, and so you might as well inform your users why their system is not at "full capacity" (in reality, this optimization process is quite rapid and quite resource thrifty, except on machines with spinning platter storage.)