I can see that what you're saying but somehow it feels more in character to me for Merlin to be mentally rhapsodising about Arthur's looks, rather than the other way round. I suppose that could just be the effect of the many fanfics you mention.

It's not that Merlin's not physically attractive, he is, but to me it seems as if Arthur's probably more interested in his loyalty, his friendship and his willingness to point out when Arthur's being a prat - after all, he's the Prince, if he just wants pretty there are probably a lot easier conquests.

Whereas it seems to me that Merlin is hero-worshipping Arthur, even though he's aware of his faults, and his looks are part of that, as well as his hidden depths. :-)

Maybe I'm just rationalising, but it all seems to make sense in my head.