The actual effect will depend on the situation. If the beholder has acquired a number of noisy minions (shriekers, if nothing else), it can be a devastating opponent as others have pointed out. HOWEVER, a rogue at the levels you are discussing will likely have move/sneak skills of 17 before magic, which could easily take them up to 27. This holds up well to the beholder's spot of 20. Even if they can't dodge the antimagic cone, the 17 vs 20 is a calculated risk.
Even though beholders can't be flanked and few rogues know how to sneak attack a beholder, just knowing where the beholder is can make all the difference. If your party happens to have a "blaster" item (high-level wand of fireballs, staff of whomping, whatever), the rogue might be able to soften up the beholder during the surprise round while the other PCs get in position if his use device is good enough.
Like most encounters, it all depends on how aware the opponent is and how well the territory favors them. If the players can get the drop on a Beholder (and know they will be fighting one) it can be over with a few well placed spells or ranged attacks. The other way around will likely result in a messy fight with several PCs seriously messed up (disintigrate & stone to flesh leap to mind).