Admittedly this isn't Injustice-exclusive, as such, but it's mostly in NRS games that this crops up.
Now, just to clarify early on, I don't have a problem with instant-air projectiles in and of themselves. However, it has to be said that NRS's method of balancing them is less than stellar at times. In both MK9 and Injustice, certain instant-air projectiles can make it very difficult for certain characters to approach at all. In at least one case as exposed recently (Zod vs Lex), it can be almost literally impossible to move at all. This has led to a lot of 3-7 and 2-8 MUs over the years, and that... that isn't good.
But what about if instant-air projectiles hit airborne opponents only?
Even with the caveat that they automatically whiff on grounded opponents, they're still very useful. They usually have faster recovery, they're still good for air control and discouraging jumping and often are very useful for building meter too. But if they only hit airborne opponents, it means you couldn't simply instant-air projectile all day and stop them from approaching, since then they can just dash forwards and not get hit. You can still make approaching annoying for them, but not difficult to the point of ridiculousness.
NRS have already (belatedly) realised that mid instant-air projectiles are a massive no-no and removed them - why not go one step further and make them only hit opponents in the air?
And I do realise that for certain characters, such a measure is rather unnecessary - Kitana, for example, has instant-air projectiles and is pretty well-balanced. But IMO, certain characters struggle with instant-air projectiles beyond a point which is reasonable, and changing all of them up to be able to deal with instant-air projectiles has a high risk of making them heavily overpowered. With that in mind, air hit-only instant-air projectiles seem like the best compromise.