So, I have finished the game and throughout it I managed to get 29 APO slots for each aspect of the car.

How do I get the 30th? Getting the APO slot itens in the last race before the final mission won't let me go past 29.

Do I have to find'em in the final mission?

I just tried it. Indeed, you have to get it from APO bonus items in the final mission.

It's actually fairly easy. There's a Bonus Armor Slot item in the cave area with an island in the middle of the red stuff lake (to the northeast of the level). You can go there very easily from the start, just look for a hidden passage to the right it the first corridor inside the facility.

Once you pick it up, just "abort the race", enter it again and pick up the same item. The game won't save any APO you bought, but will save the extra slots you got. Every time you pick up the same item, it will give you slots for a different thing if you already are maxed out in armor, thus, you can max out all three of them.