We have 5 ship positions (pilot, weapons, repair, etc) but only get 4 crew, is this intentional or am I missing something?

I'm reasonably sure that you've confused your "crew" with your landing party. It's true that your landing party can only have four people in it, but you can have a total of ten crew. Just assign the crew you have to the ship assignments to best fit their skills, and then hire more NPCs with the skills to fill in the missing positions. As you go up in level, you might also hire new NPCs to replace the ones that haven't been pulling their weight, since the skills of new NPCs are tied to the level of your main character. If you have an NPC that's fallen way behind the rest, dump the slacker and hire someone new.

The default key to see your crew roster is 'J', although you can change that in the options if you prefer.

Thanks for the info. Just tried again and it seems to be letting me recruit now, didn't at the start. Maybe reloading the game helped whatever caused the issue.

I still don't understand why we can have more than 5, moreover that the surplus will not train.

Well, first off, the main character is the only character that MUST be in the ground crew, and it isn't necessary that you hold ANY position on the ship crew, so it's conceivable that you could have 4 people (including yourself) trained in combat for the ground crew to perform missions, a different 5 people that run the ship, and another person whose only purpose is to get the best deals when shopping. Since that NPC wouldn't need any combat skills, you could put EVERY attribute point into charisma and get better money than an NPC that was splitting up the attributes more reasonably (to be more survivable in combat).

That adds up to 10 characters (You and 9 NPCs).

Currently, there is no reason you can't have the ground crew also manning ship positions, but it was my understanding that the developer MAY intend at some point to have things happening onboard your ship while your ground crew is actually doing things. If/when that is ever added into the game, you'll actually need the 4 ground crew to be different NPCs than the 5 ship crew, and a full roster of 10 will only allow you a single spare NPC to swap out for unusual situations (like if someone gets killed - I'm not even sure if that's possible right now, but it might be in the future)