I find it interesting that a number of people have said andy collins said hp don't change.. when I very well remember a thread where he said they do. However that was a while ago and I've lost the link.
HP not changing tho just plain doesn't make sense. Thats like casting a bulls strength and saying "well you can carry more now but your chance to hit and damage are remaining the same, sorry". Stats modify abilities, its the whole point of them.
Alter self is worded poorly. The quote is as follows: "Your class and level, hit points, alignment, base attack bonus, and base save bonuses all remain the same."
Note that hit points is lumped in with base attack and base saves. There is no terminology for "base hit points". Thus simply hit points. The intention seems pretty clear that your base saves are modified by your new stats, your base attack is modified by your new stats, your hitpoints (from class levels etc) remains unchanged by is modified by your new stats. Alter self doesn't have new stats so it can get away with shoddy wording. Polymorph however, does.
What would happen if you found a creature with the racial bonus feat toughness? Alter self says you gain racial bonus feats. Would you really deny that extra 3 hp because "hit points don't change" ? When it says plain as day that you do infact, get the feat?
Anything else that modifies con also modifies hitpoints, such as barbarian raging, dwarven defender in defensive stance, etc. Ability scores modify stats. Its the whole point of them.