These little "micro" states sure got a good deal with the advent of the Euro didn't they? Non membership but proximity to a nearby entity reap untold rewards. Not even sure why they can make Euro denominated coinages in the first place since their coins never circulate anyway.
The three (MC, SM, VA) had similar monetary agreements in the pre-euro years: Monaco had one with France, San Marino and the Vatican had agreements with Italy. The current monetary agreements basically continue that tradition. All three have issued coins (franc and lira respectively) before the euro came, and in my opinion it made sense to allow them to do that with euro cash too.
And quite obviously hardly anybody cared, in the years of the franc and the lira, whether any of these countries issued its coins at face or not. (SM and VA even issued entire sets of "circulation" coins with new designs every year; something that they cannot do with their euro coins.) But then, about ten years ago, people all over the world suddenly became aware of the three, and of the fact that they are allowed to issue euro coins. Boo, how unfair of them to do what they have done for decades ...
The good thing about collecting coins is that we are free to set our own goals and decide for ourselves what a "complete" collection is. For example, you can always say that you don't collect any coins which are not issued for circulation. Or, specifically with regard to euro coins, you may decide that you only want the coins from EU member states. That will automatically leave the three out, and also take care of Andorra - in case AD makes a monetary agreement some time in the future.