Of course nickle and diming the player base may have an adverse effect. Not everyone is happy with a sub AND an item store. Especially when it starts selling non vanity stuff.
I think with all these sorts of games losing players the developers have looked for ways to make up for that loss, WoW now does sub and item store, others like Rift are in effect free to play but have a very extensive real money item store, a lot of the "free" games also have an optional subscription plan which gives lots of free girfts and extra resources from gathering,reward charges etc, and often a discount from the games real money item store.
I agree that the main problem with this is when they start selling things that the game should have anyway, or advantages and gear that make it so people feel without paying out at these shops they are at a real disadvantage in the game, or "pay to win" as its known, I actually quit WoW a year ago partly because of paid level boosts surrounding me in PvP battlegrounds with newly minted top level team mates who had no idea how to play their class.
Currently the only things the UO store sells that annoy me personally are:
Mythic character tokens.
This is just a personal dislike of mine for paid shortcuts to end-game, I think its detrimental to keeping players as the process of making a new char and the "adventure" of working your way up helps to make a bond with the game, I once used a free boost in a new game I tried, I missed almost all the content and got bored very quick, I regretted being lazy and wanting instant gratification.
Improved rock hammer.
When they introduced the ability to mine just stone I thought I would finally be able to make gargoyle equipment as easy as I make human/elf, I was annoyed to see the setting was basically like having the axe set to "ore and stone" as you get the stones about as frequently as that setting, but dont get the (still useful) ore, then to see them selling the thing I expected "stone only" to be for real money, that was annoying.
We dont really know what the bottom line is do we, whether its cashing in or becoming necessary in order to keep the game viable, EA arent that sentimental when it comes to dropping stuff that doesnt pull a profit, and if this is the price for keeping UO alive, I would personally pay it gladly.