What would they do otherwise to make it harder? I can only think of to make them more agile (that's definitely frustrating) or have higher health which might be ok.
Make them perform evasive maneuvers more often so that you need to be more careful with setting up a good shot? They're perfectly agile, but sometimes, they fail to even try to avoid really easily avoided missiles. Upping the damage on enemy missiles would also be fine. There are certain encounters in the game where the AI uses genuine dog fighting techniques to trick you and get a good hit on you, and while I understand that some level of uniqueness need to be retained by these encounters, taking some of the elements from them and adding them to the standard enemies wouldn't be a bad thing. Additionally, making enemy missiles harder to dodge would be a better alternative to spam.
I played Unsung War and Zero on Ace difficulty whenever possible, meaning one missile hit meant a full mission restart, however, they didn't spam this amount of missiles. I'm not exaggerating when I say that some of the large scale encounters in 7 on Hard has such an insane number of missiles being thrown at you that you can hardly ever fly in a straight line, and that simply isn't fun. There are specific story related sequences where it fits in, but during standard gameplay, where you have a time limit to adhere to, and no real AI allies to take some of the pressure off of you, it's frustrating.
My rant came after having died twice in a row in the very last seconds of a 15 minute destruction mission, wherein the vast majority of both runs were spent listening to the missile warning siren and constantly trying to dodge while also fulfilling the point quota. The mission itself, mission 15, is brilliant, but it's not fun constantly having missiles on your tail. I wouldn't say it's challenging so much as it is just frustrating. The missiles themselves aren't hard to dodge, but destroying enough targets within the allotted time while constantly having to dodge them, is. It's cheap difficulty as far as I am concerned. On my last failed attempt, I had 10 seconds left, and were just 100 something points off of the goal. I was out of missiles, so had to use the gun against a Rafale, and I succeeded, but just as the Rafale blew up, so too, did I. The only reason I was out of missiles, was because the constant missile barrages made it impossible for me to actually position myself properly. Instead, I just had to let loose whenever I had tone. That is not fun challenge. It's BS.