Welcome Ruaridh. The thickness and quality of the leather will vary, particularly near the edges, but in the main it will be the stated thickness.
It also depends on the type of leather you'll be using; marks will show up more on russet than on bridle. They're also less noticeable on darker leathers.
It has been suggested that between 15% (for less high end items) and 35% (for high end items) of a given piece of leather will not be up to the standard required for the job in hand as there will be parts which have marks or blemishes which you can cut round. Sometimes, a mark can be made into part of the design (not often) or striations, such as found on a piece of shoulder, can be included as part of the 'character' of the leather. Offcuts can always be useful for places where the quality or aesthetic doesn't matter. They are also useful as glue spreaders, spacers, test pieces, thonging and so on.
Having patterns that you can lay on the leather to plan your cutting scheme will help..
Would write more but need to away.
Hope that helps.