#1
I'm having a lot of difficulty hitting notes past the 12th fret on the low e and a strings with my pinkie, without bending my wrist at an extremely uncomfortable angle. So far this has only been a problem with practice exercises, but is this likely to cause any difficulty down the line, and is there anything I can do to lessen my problem?
#2
Try it on the low B on a 6-string!

I don't tend to fret many notes on the low strings with my pinkie anyway, but maybe wear your bass higher (assuming you're standing)? I also don't tend to fret notes up past the 12th fret on the low strings either, preferring to fret them on higher strings and lower frets. So whether it's going to cause a problem down the line is really up to you and your playing style.
#3
Yes! There is something you can do about it! The best advice is to look (ahead of the time when you switch positions) down the fretboard and SEE where you are aiming to place the next fretted note! If you do this, you will find that your major shifts on the fretboard are FAR more accurate and smooth than ever before! Try it. I assure you that it works!
"Maybe this world is another planet's hell?" - Aldous Huxley