I guess the idea is that cybran have other advantages, like destroyers that can fight on water or land much like said hover units can.
Of course, it's not as good in practice as hover tanks or artillery (most of the time), but that's the idea, I believe.
That 'destroyers walk on land', combined with UEF getting naval jamming and cybran getting naval stealth, are, I suspect, the reason those factions don't get hover units/engineers. I believe that it's all supposed to balance out in the long run.
I'm not a terribly experienced player, so my struggles against jamming and stealth when it comes to destroyer+frigate combat might be simply a sign of my low skill; but I imagine that's the idea behind no hover T1 / flak. If I really, really wanted hover stuff in T1, I'd pick aeon or seraphim, and if I wanted the intel (and by extention, naval range) I'd pick cybran or UEF.
As it stands, I only pick random. I'd be very interested to watch replays/games where the lack of hover units hamstrings cybran, because I've not seen it so far, but totally believe that it happens, and would love to see examples to prepare me.
Do you have examples?