How much flavor do you lose when you clarify a stock with an egg raft?
I'm open to correction, but in my opinion,the main reason for clarifying a stock, assuming gross impurities have been removed,  is aesthetic. Not forgetting that the the appearance of food does change the impression of flavor. Floating ingredients can be shown off in clear soups -  a sufficiently concentrated consommé, made with a large amount of meat per helping, can have knock-your-head-off intensity. In my experience, I have never clarified a stock, by whatever method, without a sort of 'thinning' or 'flattening' of the flavor. Not so much a loss of intensity or aroma (that has more to do with the reduction) as a loss of 'roundness' I think that is probably due to a loss of fat in suspension. 

If I'm clarifying a stock by the egg-white method, I add a mirepoix (celery, carrots, leek are obvious candidates) but I shred or grate the vegetables rather than dicing them. This means that they can create a sort of fibrous mat with the egg-white when it rises, holding it together in quite a strong raft. You can then make a hole in the middle of the raft. At a very low simmer, convection then causes the stock to rise through the hole, spread across the raft, and sink again at its edges. If you're very careful, the raft can be removed in large pieces.

An alternative is Heston Blumenthal's freezing method, which he claims does not reduce flavor at all ( who am I to disagree? ... but I do..). It is very convenient. Chill the stock, remove solidified fat, freeze the stock, and then let it thaw through coffee filter, or tripled muslin. There is less waste, so you could clarify part of your stock that way, without so much of the loss that follows from clarifying small quantities by the egg-white method. 

If it was me, I would clarify only the amount I needed clear stock for, and I'd go for the second method. That way, if you freeze your stock anyway, you can make your mind up whether or not you want it clear closer to the time you use it.