I think the solution to this is offering more 'rate' graphs in addition to 'totals' graphs:
1. why not have the option to filter charts by 18- and 9-hole rounds? This way, 'totals' graphs would remain relevant based on the number of holes played and you could eliminate the need to double stats for 9-hole rounds.
2. adding more graphs for 'rate' stats would allow for comparison of all rounds regardless of the number of holes played. For example, instead of having a graph showing total fairways hit, pars made, etc., the graph could instead display fairway %, par %, etc.
Thanks for the great site!
edit: also, as an aside, the 'fairways' graph is not currently doubling its totals for 9-hole rounds while all other stats are.