You can raise an animal companion's Int with the +1 per 4 HD ability score increase. That doesn't drive it away. Casting awaken on it does break the bond, and presumably would for a bonded mount too.
The reason that an awakened animal no longer serves as an animal companion is because the spell specifically states that it does not. It has nothing to do with the animals INT. The real reason for this is game balance. Awaken does more than just increase an animals INT. They also gain +1d3 CHA and more importantly it gains an additional 2 HD. It also becomes a magical beast instead of an animal. This means its HD increase from 1d8 to 1d10, Its BAB becomes full instead of ¾, it also gains darkvision and low-light vision as well. If the spells did not cause the animal companion to leave service all druids would cast this on their companions for a huge boost.
Animal companions (including bonded mounts) are not normal animals. Depending on the level of the character and the animal they are often much stronger or weaker than a normal animal. A first level druid’s tiger is significantly weaker than a normal tiger. But at high levels the druids tiger is a lot tougher than the normal tiger. On the other hand a 1st level druid who chooses a eagle have a companion that is a little tougher than the normal eagle, and once the druid goes up a few levels the druids companion is much stronger.
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Paladin mounts are about the same and addressed in Ultimate Equipment
Sentient Companions: A sentient companion (a creature that can understand language and has an Intelligence score of at least 3) is considered your ally and obeys your suggestions and orders to the best of its ability. It won't necessarily blindly follow a suicidal order, but it has your interests at heart and does what it can to keep you alive. Paladin bonded mounts, familiars, and cohorts fall into this category, and are usually player-controlled companions.
Even without changing the BAB to full it still gets an extra 2 HD and all the benefits from those HD. Most combat worthy companions will have a decent CON score so the extra HP will be higher, probably around +15 or more. The point is that the reason awaken causes it to lose its companion status is that it is a free power up. If it was allowed all druids would cast this on their companions once they reach 9th level. Since the duration is instantaneous instead of permeant that means there is no way to counter it except for killing the companion and preventing it from being raised. No spell should permanently boost the power of a class ability beyond its base without a way to counter it. A spell made permanent with Permanency can be dispelled, Awaken cannot be.