You can see Santa on top of one from parts of Enoshima beach, which makes for a rather bizarre sunbathing experience.
I’ve always assumed it’s because Xmas day is the chief day for romantic meals and love hotel trips in Japan, even more so than Valentine’s Day (which is mainly taken up with distributing giri choko to your colleagues). According to Japanzine, however, it’s because there’s something pervy about Santa:
The thing I really learned from that article is that they are all part of one chain, so the alternative explanation is that it was a random business decision and that there’s nothing cultural going on at all.
More on Japanese Xmas:
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Photo stolen from here.