Those are different missiles. You don't need an ICBM with a MIRV to take a missile base out. That's what short- and medium-range missiles are for. Russia has those, and they don't have any better use for them anyway. The missile has CEP of 5-7 meters which makes conventional warheads sufficient; but of course Russia has nuclear warheads for those missiles as well.
And since they are by their nature the best defended places, you are going to need a bunch of missiles to take them out.
It may be difficult to attack those sites with infantry. However a mere 100 kT nuclear blast will ruin the whole day on any missile base. The radar site in the Czech Republic is a sitting duck; you can't put those antennas underground.
Because fake missile sites are cheap as heck but you can't take the chance of missing one so you need to hammer them all.
Actually missile sites are very expensive to build, and since Russia has spy satellites it can easily detect how much construction was done on this or that site. And even that is needed only if Russia has no spies in its backyard and doesn't have a clue what's up.
Also missiles are easy to retarget, so you never know which bases will be attacked. Missiles themselves are dirt cheap as missiles go. It's largely a fuel tank, some servos and some electronics. There is nothing inherently expensive once the R&D is done. The nuclear warhead would be the most expensive part.
However, all that said, I believe these missiles serve as blackmail of hosting nations. Medvedev essentially says that European countries who host those bases are now targeted, and who knows, perhaps a missile or two, assembled by a drunken worker, will deviate from the course and end up striking Warszaw or Prague. So choose your friends wisely.