It seems that you are equating number of ancestor feats per clan to number of ancestors per clan, which is not the case. The ancestor feats represent only a subset of all ancestors of a clan that are, in a individual basis, more active in their dealing with the living than the rest. I cannot get a cite regarding the number of ancestors in existence, but if you dig L5R lore about the batle of oblivion gate...
legions of ancestors were destroyed during the batle, and thousands
more of them were forcibily resurrected and thrown in the mortal realm
due the destruction of the gate
So you can infer that the number of ancestors in existence is way higher than the number of ancestor feats in existence. Also, the ancestors featured by the feats do not necessarily represent the standard composition of a clan with regard to professions, skills, etc. Two examples from the oriental adventures book: the yasuki ancestor in oriental adventures is a pirate, while most of the family are merchants and diplomats. They may have a reputation of ruthless merchants for sure, but most of them prefer outsmarting the crane merchants rather than to rob them. Furthermore, one of the crane ancestors is Yajinden, unrepentant practitioner of dark magic and creator of terrible dark artifacts, who has caused more deaths with his creations than many armies, and that achieved inmortality by stealing other people bodies. But he is the only representative in the list of the Asahina family, widely known for their extreme pacifism and respect for life.
Note that, even without an ancestor feat, many samurai still claim a spiritual connection with their ancestors, and some of them hear, or believe they hear, the faint whispers of the departed guiding them. Reverence to the ancestors is part of the rokugani religion, and is deeply rooted in the traditions and beliefs of everyone. The ancestor feats represent a special circumstance in which a specific ancestor has decided to give one of his/her descendants a special blessing.
Not every descendant of Doji has the Doji ancestor, because story-wise, no one "claim" doji as an ancestor. You can claim belonging to the doji bloodline, but it is Doji herself who decides who between her descendants is worthy of her favour, not the other way. Oriental adventures do not have examples of NPCs of note, but the rokugan campaign setting contains some important guys and many of them do not even has ancestors, and those who do have ancestors that do not necesarily match their family/clan. If you can take a look to the NPCs of other editions of L5R, you will notice that not every clan/family daimyo has their family ancestor, or any ancestor at all.
As an additional note, in some editions edition at least, some ancestors could actually retire their blesing if their protegees did something to anger them. The mirumoto ancestor, for example, would leave those that abandoned the mirumoto kenjutsu school, the Hiruma ancestor would abandon those samurais that become too honorable for his liking (he was a brutally pragmatic guy), and the Isawa ancestor abandoned any shugenja that lose a magical contest or duel against a non-isawa.
Also, note that the guidance of the ancestors is often subtle, and the ability to sense the presence the departed is quite rare. Even moreso the ability to actually talk to them. In fact, such ability is often limited to the small kitsu family of the lion clan, and they do not share it easily. So is perfectly possible that a samurai is not aware at all that he is specially favoured by his ancestor. As a example, many akodo samurai can claim to be guided by Akodo, but there is a loooong way between faithfully believing to be guided by an ancestor and having factual knowledge that you have the personal blessing of the lion kami. And there is a even longer way between knowing it and being able to prove it to others. For that reason, the number of ancestors feats has nothing to do with the prestige/status of a clan. The blessing of the ancestors, while powerful and significant, are a way too spiritual issue to have any political weight at all.
Finally, the part about not being "limited to choosing ancestors from their own clan": Intermarriage is indeed common in Rokugan, but the tradition says that the member of least status is absorbed into the his/her consort family and clan, cutting all ties with his/her former family and clan, at least officially. In this situation, it is safe to say while many samurai married into another clans will usually keep venerating their old clan ancestors privately, their sons and daughters will be educated to venerate the ancestors of the clan that adopted their parents. What does this mean respect to ancestors feats? As much or as less as the specific ancestors want it to matter, because, story wise, they are the ones who decide who receive their favour or not. So, yes, in oriental adventures a player can select a phoenix ancestor for his crab samurai, for example. But in the first editions of L5R, these type of things would require the player to get create a good story for the character to justify it.