I tend to agree with Antony. Though I don't have a strongly-held view about whether armature drivers as a class may enjoy burn-in effects or not, my three concurrently-owned pairs of ER-4S's, of varying ages, have always sounded the same to me given new filters, and so I tend to feel that the ER-4S, at least, is not significantly affected by burn-in.
The 4B might be different inasmuch as it contains capacitors. However Etymotic seems like the kind of company to choose components that will remain stable over time and use. (Read some of Etymotic engineer d_wilson's posts here and on headwize to get a sense of the sort of engineer he is.)
As to the green filters, they absolutely do age, and the audible effect of this is some muting/rolloff of the highs. For me this means it's time to change filters and get my (and, I believe, Etymotic's) idea of 'correct' sound back. But I could imagine someone with different preferences using this as a way to customize the sound a bit: get a new set of filters, arrange for them to get clogged up to the correct degree, then enjoy the music.
That seems like an awful lot of work, though. If you find the highs of an ER-4 harsh -- especially the ER-4B, which goes to extra effort to emphasize the highest highs -- then it seems as though a different earphone would be a simpler solution. If you're happy with a well-broken-in ER-4B (or an ER-4B with well-broken-in filters) then I won't by any means gainsay that for you; but I would be pretty reluctant to recommend it as a general solution for new buyers.