Thinking about it, restricting the number of riders who count towards the national standings does make sense, because:
a) counting the points from all riders would tend to favour big countries with a number of possibly average (in terms of the pro tour) cyclists
b) the national standings are used to decide the number of riders each country should get in the world championships. The rankings should thus reflect the strength of the team you could expect from such a country, so counting the best 8-9 riders in a country seems reasonable (I know that those would not in general be the riders in the world championships team, but what can you do, it would probably ensure at least a range of types of decent riders in the highly ranked countries). Raising the number from 5 is also likely to work against e.g. a small country with two brothers who earn masses of points, but unless the worlds are in the alps or Columbia might as well be down the pub. edit: OK possibly on the LBL course or something similar
Counting the results of a small number of riders in the pro tour teams does not make any sense because:
a) they all have to take a team to all the pro tour races, thus there is no large team bias (there's not a lot really you can do to counteract differences in budget).
b) it might work against young talented riders who do not get a chance to lead a team if it appears it is struggling in the rankings