What happened to them that now they can't even reach 100k for their single
That's a good question for which I think there's no "right" answer. There are some factors that could have contributed to this: some changes in their sound (it was probably the cause of their abrupt drop in 2001), changes in the interest of general listeners (rock was not "in" anymore in Japan), or even the problems they've had with management/record companies. But it's hard to say that the reason was really "this" or "that". My guess is that most artists are bold to see their sales decline eventually. How Mr. Children managed to keep it so stable for that long is more of a mistery, to be honest LOL
I don't think GLAY's case is abnormal when you look at the general scenery. Their sales are nothing like they used to be at their peak, but they are still able to reach top 10 weekly every time (in fact, with the exception of three "rare collectives" volumes, they've always peaked at #1 or #2 since their first #1, which was in 1996). Then there are some other artists who also used to have huge sales and to hold records in the past but now have very low sales and don't perform well on Oricon. Even so, some of them are still considered stablished artists or even have reached the status of "legends".
I would love to see GLAY having a huge hit again, but I don't see that happening. The fact that they are now under their own (independent) label means they are hardly going to have any important tie-up and other types of big promotion that would be really effective in making their new music known by general listeners. Their pattern is different now. But GLAY have been fairly stable with sales. They had large drops between 2000-2004. However, their latest original album, in 2010, didn't sell much lower than their previous one released 3 years before. Similarly "LiB" didn't sell much less than "The Frustrated", also released 3 years earlier . Their sales would probably look more stable if they released original albums more often; from 2004 to 2010 they released 3 original albums while some artists released one original album every year.
Considering that their sales are still decent, we don't have to worry about them
And when they decide to retire (which will eventually happen), the cause won't be the sales.