...why is it generally frowned upon?
Its a matter of gameplay preference.
Players in AH generally break into two groups:
1.) Those who go looking for a fight.
2.) Those who try to avoid a fight.
There is nothing wrong with NOE missions in and of themselves and, in many cases, they are the tactic of choice when you wish to take a base.
However, by their very nature, they are designed to elude enemy detection and, thus, are more focused on avoiding a fight than creating one.
While this makes perfect sense from a tactical standpoint, some members of the community feel as though it defeats the purpose of logging in in the first place.