YES, if there is an ability that lets you make skill checks for your mount, as you posit in your question.
Hide in Plain Sight lets you make certain checks in situations you otherwise couldn't. It doesn't, on it's own, let you hide your mount, as a mount is a separate creature. You could use the skill while riding it however.
If you are, via another ability, allowed to make skill checks for your mount, you would then be able to use Hide in Plain Sight in conjunction with that ability to hide your mount.
To prevent misconceptions:
Familiars and many other similar creatures (like mounts ridden by a Wild Plains Outrider) can make checks using their master's skill total. They are still making the check, however, and thus don't benefit from their master's Hide in Plain Sight, should he or she have that ability.
Small as Mice:
A few rare abilities in splatbooks (such as the spells Small as Mice and Silent as Rats from the third party Book of Roguish Luck) allow for group hide checks to made. All of the examples I have seen phrase this as "the group makes a single check based on your skill modifier". If this was instead phrased as "you make a single check for the group", you would be able to apply Hide in Plain Sight. As it is, you may actually lose Hide in Plain Sight when you cast this spell, as the hide check is made by the 'group' and so Hide in Plain sight would only apply if the 'group' had it. It is most probable that abilities modifying your stealth roll will need to be applied to each member of the group in order for the 'group' roll to be modified. This is an extrapolation from the rules, however, and your GM may very well rule that if any member possesses an ability the 'group' roll benefits from it or that if at least half the members possess the ability the 'group' roll can benefit. A particularly interesting possibility is adjudication similar to Shadow Evocation, such that whether or not each ability applies is determined by a d100 roll and the percentage of the group with access to the ability. In any case, with the wording the way it is now, this basically comes down to GM discretion as to what the 'group' having an ability means.