Yandex did have a Dutch datacenter when it planned the expansion in Turkey (and other countries later). That expansion didn't work out and that datacenter was closed.

Taking that aside, I wouldn't say that Yandex is incorporated in Netherlands for tax reasons anyway. (It actually pays most of its tax in Russia anyway).

It was created for legal reasons though. AFAIK its ownership structure (with 2 classes of shares, with different voting rights) was illegal in Russia at the time Yandex went public.

Many Russian companies used foreign registration to prevent raiding from corrupt higher-ups. It was kind of rule, at least in IT companies. For example FSB forced Durov to sell vkontakte. It wouldn't happen if vkontakte was registered outside of Russia. I don't know whether that reasoning was applied to Yandex case, but I wouldn't be surprised. Another former Russian company is Jetbrains which used to operate from Russia for a long time, but their company was registered in Prague.

I wonder if Yandex eventually will be forced to completely move inside Russia. It seems that their Russian operations are main revenue source and they probably would not be able to leave Russia. And with current events unfolding, wall between Russia and Europe will probably only rise.