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The pic is a little confusing, because it looks like there is a shadow of the E, so it doesn't actually look like it's into the fingerboard. From how it looks to me here, it looks like it is notched deeper into the nut than the heavier strings, which probably isn't unusual so long as you have at least a millimeter or so of clearance between where the string leaves the nut and the fingerboard.
If it is actually into the fingerboard itself though, I think that would be a problem eventually. If it is all the way to touching the fingerboard because it has cut through the nut (or the groove was cut too deep) that may not throw off the intonation at first, but the tone of the open string would be affected and you might get some buzzing. If it cuts into the actual fingerboard, then your intonation is definitely going to be getting thrown off.
Again, if is it just a bit deep in the nut, and not actually touching the fingerboard, so long as it isn't buzzing, that is probably normal enough.
"This young wine may have a lot of tannins now, but in 5 or 10 years it is going to be spectacular, despite the fact that right now it tastes like crude oil. You know this is how it is supposed to taste at this stage of development." ~ Itzhak Perlman
Oliver you hit the nail on the head.
If the string is too low and cutting into the nut then a simple thing would be to take the little plastic tube on the E string that you usually put between the bridge and the string and put it between the nut and the string. This will raise the string slightly and help prevent further cutting in until you can get a new nut made.
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