Yes, bolts will often hit even if they are not "supposed" to. Beams will be guided by the animation process to deliberately miss if the "to hit" code says they must miss. Fighters are small and so less likely to get an 'accidental' hit in spite of the percentage "to hit" calculation by the game engine.
Bolts are the weapon type for the point defense cannons. At short range they are more accurate. If you make them long range they miss quite a bit. Bolts are not intercepted by Point Defense Cannons unless you mod to allow for bolt target. However I think by doing this then you would cause a fire issue everytime a bolt wep is fired even by you own ship. This is my experience with this.
Beams are meant to miss sometimes (reason for attack and defense ratings)