My take on this is this...
1) I do not expect rubber to win against grit.
2) I would run some gaiters (just like the old days) or wraps (kriegas) if I was going to do huge amounts of dirt / mud.
3) I would try a clean first. As with dirt bikes the crap tends to push out the seals.
4) Have they failed or just become clogged. If they are cleaned and they are back to normal well then use a Kriega or equivalent for long trips.
5) I would hassle the dealers and YAMAHA because having a good think about the bikes "issues" and good will, will always be better than having no idea there is an "issue". YAMAHA may not have expected the kind of use these bikes are getting (although the seal thing I would say they should have). Try and make them pay as this is a better persuader of management then anything else. This will appear on P&L's every month and can be directly traceable where as "good will" is a bit airy fairy for accountants, until they go and try and sell the company. I think the marketing department thought that Starbucks was going to be the prime destination, while the engineers were fuming in the background.
5) They may update the front fender and seals at a later date if that is the case. I mean what power does an engineer have in a company really. It's all their fault anyway.
YAMAHA may threaten to switch suspension suppliers if they don't fix it.