Some days my goal kicker just couldn't hit the side of a shed, and some days he slots everything from every where. As he is always playing with between 95-100% energy that's not the likely cause, but I wonder if match fatigue is?

All other things being equal - is a kicker freshly subbed onto the field more likely to get a kick than a guy who has played 75 minutes?

Yes energy definitely affects kicking. As time goes on, you'll train kick accuracy on your main kicker a little bit, but the game actually sorts out the randomness as well. You kick a little better with each season basically. The bizarre kicks to the corner flag become a thing of the past once you progress to around lvl 20 I'd say (with the occasional comical exception).

I would add that the game uses kicking as a means to stop you beating teams you shouldn't beat. At least that has been my experience. I miss kicks against teams much better than me when a penalty would steal it for me. Maybe that is my imagination though...