The title of the question says it all: wondering why the icon has an L, instead of an I? Is this a mistake by SE's designers, or is there a reason behind it?
It confused me quite a bit, as I don't know much about Iota, and so until I spotted the URL of the site I thought it must be Lota with a lowercase L!
That's not an 'L' — it's the Greek lower-case iota:
Greek letter Iota Iota site logo
The reason for choosing the symbol should now be a little more obvious, given the site's name of Iota. While many Stack Exchange sites are named after products with more official logos (such as Iota's logo), the official logos are often not used — presumably, trademark licensing is a large factor here.
#/media/File:Iota_logo.png){kind=link}
ι - guess it's a font thing