The percentage-nomenclature is something that I believe appeared here in the keyboard enthusiast community and only in the recent decade. I believe it may have come from the number of keys, classic "full-size" keyboards having close to a 100 keys. For instance, the
Happy Hacking Keyboard has 60 keys, and is a "60%" keyboard. Some other keyboard models have had their number of keys in the model name.
Smaller keyboards are indeed to save space and to move the mouse (on the right for right.handed users) closer to the centre which is considered more ergonomic.
To me it appears that users either use the numpad a lot or they never use the numpad at all and therefore don't need it .. and you can sometimes see pointless stupid forum-wars between users on "either side".
Users on this forum tend to be more level-headed about that though and more accepting of different formats.
Personally, I think the best layout would be full-size but with the numeric keypad on the
left side of the alphanumeric section. That way you could have best of both worlds, and also map some of those numeric keys to special functions in games or in various other types of software that you could press while using a mouse in the right hand.