I agree with you and your concern about adding the directive "pci=nomsi,noaer" in the grub directives to simply to suppress the reporting of errors. With serious problems, one needs to have the errors reported so we can fix them, something that won't happen with "pci=nomsi,noaer", a directive designed to suppress such valuable error messages.
I happened to find this forum thread by searching for the "no irq handler for vector" message that appears too much when I boot into multi-user.target (text only based login). The error is extremely persistent making it difficult to type commands as it pops up in all ttys even while I am typing a command.
Answering your original question; will adding the directive "pci=nomsi,noaer" in grub harm your system? I would have to say "no", that the directive itself would cause any harm. HOWEVER, something is wrong with your system and suppressing the error message itself does nothing to fix the problem and, whatever the original problem is, IT MAY (actual problem indicated by an error message) cause harm to your system.
Consider this; a man has a fever so you give him Tylenol and the fever goes away, but then he dies of a massive infection because we didn't give him the antibiotics he actually needed. Solving the error message won't help or harm your system, but ignoring the original problem, maybe!
For what its worth, I am still trying to figure out how to fix the problem that causes the error, "no irq handler for vector" that takes over my text based login. I know IRQs (Interrupt requests) are often used by hardware devices to get the attention of the CPU, and since I have been having problems with various hardware devices, the error is consistent with my hardware problems.
I hope you find a solution to your problem.