tl;dr: RTFA, not just the pictures.
Full version:
Unfortunately, you misread the site. The site doesn't report the popularity of chords by name at all. If you'd read the lead-in to the chord chart, you'd see the explanation. Or if you'd thought about the most popular chords being "G F C Am Dm Em", the main traids in the key of C, you might be suspicious. Or if you had read the following analysis on the site which explains his theories for their popularity, you'd have seen your misinterpretation.
The site reports the popularity of key signatures by name.
It reports the popularity of chords by pseudo-name: relative to the key signature by transposing all the songs into the key of C. Yes, that's a dumb thing for him to do, but that's what he did, and it's identical to what you propose he should do. (The per-song analyses do actually use roman-numeral notation.)
Your explanation is therefore bogus; the A chord is not necessarily particularly rare as far as we can tell. Maybe it is, maybe it isn't. Probably it is, actually, which leads me to my second argument: your reason for why it's rare is wrong.
It is absolutely true that the popularity of many chords in guitar music is due to what's convenient on the guitar. But I'm doubtful that A chords are very rare in guitar music. More likely, the pop music analyzed here is not very guitar-centric.
Let's look at an actual guitar band. The easiest to use is the Beatles, since they're well studied. They got less guitar-y in their later albums, though. Here's a source.. Note that relative minors have already been adapted in the same way.
Top six keys in order on the site in the slashdot article:
C G Eb F D A
All beatles: G A E D C ...
First two albums: E D A G ...
Next three albums: A G D E ...
Abbey Road: A C E D F
So, in this actual guitar band, before they started writing on piano, retuning songs by changing the tape speed, etc., the keys of E, D, and A were incredibly popular, so I bet the A chord was probably popular as well. (but I have no stats).
And since guitarists don't actually avoid these keys, unsurprisingly, your explanation for why guitarists would avoid these keys are wrong. (1) The B chord is uncomfortable for a beginning guitarist, but the B7 chord is easily learned, so B doesn't present a problem for the key of E. (And the reality is that the difficulty of the chord isn't a big deal for serious musicians. They favor open chords not because they're easy, but because they sound better.) (2) The key of D doesn't present much problem, as not having the chord root not at the top just means you play inversions a lot, or use sparser chords. The fact it's not low is irrelevant when you have a bassist; and look at something like Nashville tuning. Indeed, the convenience of a flexible A7 for use as V, and the ease of Dsus2 and Dsus4, makes D a quite popular key signature on the guitar. (3) I don't know why your A theory is wrong, but since your E and D theories were wrong, and since the Beatles (with three different male singers) loved the key of A, I can't imagine it's correct.
So, the actual explanation for why A is at 2% is that it's the "relative A" chord that is the major VI chord, or i.e. the V-of-ii chord. That makes it popular enough to be at 2% -- V-of-ii isn't unheard of, but not a particularly common chord in the key of C, the way the non-diminished triads from the key signature are.
