It's not a contradiction. "Major" is not the same thing as "Part of the critical path". In a game with ten fleshed-out sidequests, total, it is in fact pretty fair to call each one 'major'!
No, there is a negative opportunity cost for investing in hacking. For every point you put into hacking, you earn back enough experience through hacking to gain about two Praxis Points. Not to mention the fact that two of the three quests in question give Praxis Points as rewards, meaning that putting the... seven, I think, points into Hacking: Capture and Hacking: Stealth results in you gaining somewhere in the area of 14-16 points.
Your two options are quite effectively 'do I take these skills, gain extra levels for having done so, and open up 90% of the game's blocked-off areas in one fell swoop' versus 'do I not take these skills, end up with fewer points to put into other skills, and render myself completely incapable of completing several of the game's small number of sidequests'.
It is the opposite of the RPG "agony of choice".