Yes but perhaps it doesn't matter as much as you'd think to the European airlines. Presumably Russia is charging what the market will bear in overflight fees. If flying over Russia is an option, airlines that choose to go around pay fuel/operational costs for the extra two hours of flying time, but they also must charge less for tickets, because their competitors that overfly Russia get there two hours sooner.

If EU airlines categorically can't overfly Russia, their only economic loss is the extra flying time, not the reduced ticket prices from taking longer, since their competitors are on the same playing field.

The winners in this would presumably be Turkish and the Gulf airlines.