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My first tac squad came with Dark Vengeance, so all the marines had kneepads. I put the company colours on the left knee. I'm now working through a second tac squad, and I've noticed that not all the marines have kneepads.

Do people normally paint the colours at the top of the shin section of armour, or leave them off when there are no kneepads?

I'd leave them blank tbh.

I normally go just metal, though templers lack company markings

Yeah, the more I think about it the more that leaving them alone seems like the best plan of action.

I wasn't sure what to do with the AOBR marines, so I can show you what it looks like;

http://www.dakkadakka.com/dakkaforum/posts/list/592461.page#6789774

It came out OK, but probably only because I was doing company and squad markings (5th company, 5th squad (checked)) that isn't really to codex either, I am using company markings as squad markings;

http://www.bolterandchainsword.com/uploads/1258059625/gallery_43449_4253_3399.jpeg

And making them white (sand/sandy brown) and whatever the company colour is, in this case, black. Might look weird with gold, who knows.

I would leave them blank.

You could use your exacto knife to score a horizontal line just below the top of the shinguard. There is an example of what this looks in the current tac box.
That way you still have a sort-of knee-pad to paint and keep in theme with the rest of your army.

Painting knee pads is up to the person painting them. You are the one painting them so you make the choice. Will it look good or not to you.