I think Clamp became popular because their early works were truly unique and original (at least at the time when they were released). Part of that uniqueness lying in the yaio twists they put in their stories

(big reason why some fan grrls would go into hysterical frenzy at the very mention of the Clamp name, IMO)
And they're still popular now because they experienced with quite different genres, which means most people can find among their series at least one that appeals to them.
For better or worse, their art at least is really striking (anyone claiming they can't
see what's so special about it needs a new pair of eyes

- unless they only saw anime adaptations of their works, which can't do justice to the original art, IMO) and unusual (I won't say "unique", because obviously it's inspired from classic art styles such as "art nouveau" - which is a nice pictural reference, IMO)
It's true the stories aren't really
deep. They're full of symbolism (written into words, and/or in the pictures), but they talk about rather simple, essential things. Just like poetry. Poetry doesn't need to be deep (like an elaborate lecture or a philosophy essay) it just needs to be pretty and talk to the "heart".
What I like about Clamp is that they really know their symbolism well. It's usually not just some random unconnected references for the sake of it - the whole thing is neatly tied together (like an extended metaphor) and makes sense (and the cross-references between their various series is consistent as well).
You could say they managed to create a "mythology" of their own - rooted in oriental "philosophy" (ying-yang stuff, especially), but their works themselves obviously can't be called "philosophical" : like all mythologies it just talks about simple, universal themes (=> nothing really deep, in the end, just intriguing stuff punctuated with a few simple words of wisdom)
That's enough for me. Complexity is over-rated
Also, the many silly (often parodic) series they made contrast nicely with their more serious works: it shows that as authors, they don't take themselves too seriously (despite their artistic maneurism and heavy use of symbolic references), which makes them quite sympathetic, IMO.