I don't look in every player's rune page and keep track of how many do but that's not the point. People who know what they are doing take runes like those; specific, uncommon sets of runes in specific situations.
The points are:
1: They exist to give additional options. Niche options are still options that have value. Same reason people have more than two rune pages.
These runes may even be buffed down the line; it's happened before.
2: I don't think you grasp how small the benefits are that runes provide. Runes only provide small, single digit, percent improvements.
Take flat armor seals as an example. Two armor seals will only reduce damage by about 1%. That means that for half the champions, taking two armor seals will get the benefit of being able to take an extra 10 damage at level one.
10 damage is not a lot, Leona (who gets a whopping extra 11 damage from those) does 6x that amount of damage to an enemy with a single auto-attack!
That's how runes work. You could take armor and get a couple dozen hit points saved, or you could switch out a few and get a couple dozen points of mana which can make the difference as to whether or not you get to cast an ability.