My rationale is simple - I do not see the point in a national limit for Missionaries at all. In most cases the limit isn't reached, except when you want to infect a lot of cities at once - which usually occurs when you get a later religion, or if you suddenly have a rival open their borders to you and you feel only a small window of opportunity to spead your religion before they close again.
The issues with religion that you cite are, in fact, more down to the fact that Buddhism and Hinduism are able to be founded so early from research, especially for civilizations that start with Mysticism, that you are guaranteed to get the holy city for these religions in your capital, as few players are even able to get a second city up and running at this point without a gift settler. This puts them in extremely defendable cities that takes an immense amount of effort to conquer. In addition, the headstart provided for these early religions is such that the later religions have a hard chance keeping up, and these religions are the ones more likely to hit the National Limit for Missionaries, even when they are just spreading to that player's other existing cities. By removing the limit, these later religions have a much better chance of catching up and keeping up with the earlier ones in the game.
In addition, I feel that a National Limit is more restrictive than beneficial in most games. It is a very arbitrary limit, when there is already a number of more natural limits in play that can control Missionary usage. Civilizations are limited to producing one missionary per city per turn, and more cities requires means increased maintainance for all cities. Missionary units also count for Unit Upkeep purposes, so there is an upper limit to the number of missionary units a play can have and how long they can be out for before the player risks negative treasure issues. Since a shrine provides wealth, the upkeep limits can be steadily offset, resulting in a snowball effect for religious spread, which mimics the snowball effect inherent in the fact that you can only build missionary units in cities with that religion in the first place. But most importantly, resources devoted to building large amounts of missionaries quickly are resources not being spent on other aspects of empire management, such as military units, settlers, or economic buildings.
Plus, there are many ways other players can slowdown or compete with a civilization that has a holy city and a shrine. Military pressure can be applied, forcing the religious civ to divert resources away from missionary production; diplomatic pressure to get others to cease trading with the religious civ, thus closing their borders, or to adopt the Theocracy civic to stop non-state religion spread will reduce the targets for missionaries to spread the religion to; if you want to risk war, you can even kill their missionaries before they spread the religion, although privateers raiding missionary loaded ocean-faring transports also works; Alternatively, go to war and try to sieze the holy city for yourself and claim the religious civ's efforts for yourself; Finally, you can raze cities with the religion, thus reducing the existing influence of the religion - this can be achieved by going to war with a third party that has also had the religion spread to it; if you really are mean, or don't feel you can hold a holy city for yourself and want it gone, raze the holy city yourself, and have done with it. All of these options means that the civ who founds and shrines Buddhism isn't going to automatically win the game, but rather provide additional and/or alternative antagonistic options within the framework of the story that is that specific game of Civilization IV.
Thank you for the feedback though, and I do hope this verbose reply gives you some insight into the justifications behind the changes to the Missionary, how I feel about limits in general, and my concepts and ideas for improving religion. But remember, if you really don't like what I've done with the Missionaries, then don't use them - the National Limits for units are covered by the Unit Class Infos file in the Missionaries daily mod, and can easily be ignored if you wish to keep the original limits.
(Edit: BTW, I am typically this verbose when responding to questions and stuff. Please don't consider the length of my post as antagonistic or ranty - I actually enjoy writing long forum posts where I get to use my brain a bit. Comes from my academic background of essay writing, I guess... and no, I am not being sarcastic here, either. Honest!)