Hunts aren't getting scaled HP. A Ranks aren't intended to be attacked by the entire server at once.

B's are intended to be soloable.
A's are intended to be fought by a single party.
S's are intended to be fought by an Alliance or more.

This is the way hunts were originally envisioned by SE. They tried boosting HP(B's needed a light party and A/S were just bumped up a bit but not enough to require more people) soon after the hunt started when they realized that people weren't doing it correctly, but it didn't work. They then switched to B Ranks being worth nothing except weeklies and the rest were left alone. This got it back closer to the original ideal of B Ranks being the fodder of casual players who would just find one once in a while and get some seals. Now the casual player was able to take that 100 seal weekly and also do dailies that were boosted in value to get their upgrades. Unfortunately, this also didn't work because it took weeks to get even a single upgrade item. Heavensward does the daily/weekly dichotomy much better as it now takes 2-3 days to get an upgrade item so a patient player can fully kit out one job in about 3 weeks. A great compromise for players unwilling or unable to participate in the A/S Rank zergs.

So A Rank Hunts are actually fantastic little pieces of content when they're fought with the correct number of people. They actually have mechanics! As previous replies in this thread have surmised, there is no way to "fix" hunts at the killing the monster stage without making things needlessly complicated to the point of excluding the casual or possibly even the mainstream population. Furthermore, any attempt to fix things can and will be abused by the hardcore crowd to the point of the additional mechanics doing nothing in the first place.

So, there is really one, and only one, way to "fix" hunts: stop putting the tome gear upgrade items as a reward.