I'm not a huge expert on guild composition in terms of every high end guild, but I believe that the lack of Moonkin Success in high end guild is probably the primary reason that guilds are not giving moonkin a shot. However, there are a lot of problems that Moonkins face especially in SSC and TK.
First of all, people don't really view Moonkin as a DPS class, but as a utility class. As a result, since Moonkin does not provide as much utiltiy as Feral spec (note I'm not trying to start a Feral vs Balance vs Resto fight here.) since Feral acts as an offtank, people are reluctant to bring them on raids. In fact, Moonkin actually puts out quite comparable DPS to mages when specced right and with a shadow priest while providing that extra 5% crit to the other 3 DPS casters in the group. For the shadow priest, crits on SW
and Mind Blast (if they use these two spells) means extra mana returned to the group. For the mages (especially Deep fire ones), extra crit means extra damage as well as mana regeneration.
Another big challenge moonkin face is the extreme lack of Leather Spellcasting gear that exist in the game (none in SSC/TK, i believe). This cause a big discomfort to the cloth casters that need to compete gear with a Leather wearer. Granted, crafted gears are probably best for both parties (the Moonkin and the Clothies), the reality that they need to compete for gear and clothies complain about it discourage raid leaders from bringing moonkins on raids.
Do I believe Moonkins are raid viable: definitely. Especially with a % party buff, the percentage returns are not declining as gear improve (versus static buffs such as Battle Shout, for example). However, it requires a extremely dedicated Moonkin (since Starfire is much more mana efficient in raids, tailored sets might be pretty necessary just as a starter set) and a very open-minded set of raiders (especially the clothies) and the raid leader.