Well thematically speaking couplers can't really have anything to do with hacking allies, but even if it might appear this way, it's not that the hacking is limited by theme, the theme was set specifically to apply this limitation on the gameplay
Future robot hacking additions will continue to be about new types of behavioral hacks (mainly NC), so not really buffs, per se, since they all come from the same coupler pool so it's all easily balanced against itself under the same system. But I wouldn't want to water down these effects just because you can also do them on allies.
Many of the hacks can be as cool and effective as they are specifically because you need to be in (or create) the specific situation required to use them, some of which may not be incredibly common. This is an important consideration when setting their effects and costs.
For example deconstruct_bot is pretty cheap for what you get, but it's cost would absolutely have to be higher if you could do it to allies, because it has to be balanced for the easiest approach, making other approaches like encountering random assault squad Mechanics less valid... See what I mean? xD
From an pure balance perspective, I don't think you'd really want hackable allies because I can tell you now the result would almost certainly mean nerfs across the board.
Note that
without any hacking allied bots (including NC bots)
do do a bunch of stuff for you. Some players love having Operators for friends, for example, because they have special behaviors (including some which you cannot hack them to do), and other allies are useful in their own ways.
