Simcraft is simulating perfect execution of the wrong rotation, apparently. And narrowing it down to three of the twenty-one DPS specs helps those who are looking; a large part of figuring something out involves learning what the possible is.

My best guess is that what Blizzard considers "close enough" and what heroic raiders consider "close enough" is dramatically different. A 5% DPS boost is more than enough for a heroic raider to respec or even reroll, whereas in any less demanding gameplay mode that kind of advantage is so trivial that you're better off just playing what you like.

Melee is getting an AP boost because they need it.
If you have ever been in melee and are a nice person or actually look at your health bar, you'd understand why. Running out of melee for "BOSS HATES MELEE AOE ATTACK THAT HITS EVERY 10 SECONDS" lowers DPS.

And almost every boss does this.

A lot.

There is indeed a gap in the data available with hunters, and likely with other 'underperforming' class/spec combinations. To use BM as an example, there simply aren't enough people playing BM at current endgame content-level to collect real data on it. As an antecdote, I'm praised for my ability to make BM work about twice as often as I'm criticized for using a 'fail' spec, at the same time, I see a lot of BM players with gear that indicates 'beginner' or 'alt' dps while their pets are on passive or perhaps take talents less optimized for damage in PvE situations or less optimized for survival in PvP situations, etc etc. MM is simply better-tuned to scale with the gear available, whereas BM and SV have their old Wrath reputations hanging from their necks in addition to current numbers.

TLDR: underperforming specs are also underrepresented in current content, so keep that in mind before declairing a spec 'noncompetative'.