In answer to your original questions,
Do discs have a standard fitting system to the hub whether motorised or standard wheel?Yes they do. It is called IS mount (International Standard) and features 6 bolts arranged in the same pattern so discs are interchangeable. Beware though that some hub motors for some bizarre reasons, use their own fitment.
Not many do thoese days but back when Ezee were the first to try it their fitment wasn't IS, and I have heard of a few who were the same.
Does the calliper have any scope for adjustment across the axis if the alignment is slightly out?This depends on the caliper mount. Some forks/frames use IS mount, which is 2 holes that look like beefed up mudguard mounts. other methods are Post mount, favoured by Manitou and the latest Marzocchi forks, these mounts bolt straight to the fork. Your disc brakes will have an adaptor to fit the correct type, and this also corresponds to the size of the rotor (the actual brake disc). Most either allow you to undo 5mm allen bolt to micro-adjust the caliper across the axis, and some (namely Hope) use a shim system to allow you to get the correct fitment. You can also use a 'facing' tool to remove fractions of mm's from the mount to adjust the opposite way. These are often used on cheap frames where the tolerances on the mounts are not accurate, or they have been painted over. The tool is incredibly expensive, although most 'good' bike shops will have one.
Anything i should observe or watch out for? Make sure your hub is 6-bolt IS mounting type, always use threadlock on the disc rotor bolts whenever you remove them, and when bolting the rotor to the hub, unsure the bolts are long enough to not rip out under heavy braking, but not too long to damage the internal thread on the hub.
Would it be better for my first build to use a bike with V brakes instead? V-brakes are more than adequate tbh, the reason discs are so popular is that they perform well in all weathers, dont clog with mud and you dont get rim wear on high mileage. If none of this is if benefit to you it's not really orth the hassle.
One other thing to bare in mind, most front hub motors are very tight on space, but the bigger the rotor you fit, the further away from the hub the caliper will be, hence the better the fit. The bigger the rotor though, and the more snappy the brake will be. Also you will need a bigger rotor and caliper adaptor. Most standard rotors are around 160mm but you can get oversized ones around the 200mm mark.
I hope that is if some help, I will stop here as my fingers ache, but if you need any help on disc setup just drop me a line. I have retro fitted enough in my time
