Assuming I'm correct to say that if I'm invisible and my mount is also invisible (separate spells in this case) then I can't see my mount, do I get a penalty to ride checks for that mount?
No, there isn't
The invisible condition applies the following:
Invisible creatures are visually undetectable. An invisible creature gains a +2 bonus on attack rolls against sighted opponents, and ignores its opponents’ Dexterity bonuses to AC (if any).
The penalties of being invisible are all applied against attackers, it doesn't affect the invisible creature in any way, or seems to affect her own dexterity or strength based checks in any way, which includes the Ride skill.
Not only that, but an invisible creature can be found by trying to touch it, as described under the Invisibility special ability. Since you are, you know, mounted on the creature, you are always touching it, and no other checks should be necessary.
Finally, the rules for Mounted Combat also have no mention of invisible mounts being an issue.