> I am wondering why it is not mentioned at all in basic text books such as Lehninger?

Books are not flawless.

> Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, > then why is histidine such a weak base? 

Pyrolles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity ([Check Lewis bases and acids](http://en.wikipedia.org/wiki/Lewis_acids_and_bases)) .

In imidazole, the other nitrogen does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is much stronger base than pyridine.

But compared to lysine `(pKb ≃ 10.5)` and arginine `(pKb ≃ 12.48)` it is a weaker base `(pKb ≃ 7)`. Imines are generally weaker bases than amines because the `sp2` hybridization of the former gives them a more `s`-like  character; this makes the lone pair to be held more tightly to the nucleus thereby reducing the basicity.

The strong basicity of arginine is because of the guanidium group.