"I'd like to know why it was thought individual damage types should get runes to protect against them, but not all individual damage types did so."

Who knows...? Personally I think adding a rune/protection type is very... boring. It makes the game seem too much like an excercise in numbers, and feels like one step away from just calling the damage types "Damage type 1", "Damage type 2" and so forth.

"How much protection is added via these runes?"

It's... slightly weird... First of the new runes add about 24 to all crit types, and 75 or so to the special crit type... Subsequent specialized runes add 61 or so to the specified crit type I guess? I'm not totally certain, but it is something in that neighbourhood....

"How many runes can be put on armour now?"

A 150% rune is about 13.5% skill... Full fortification is 46%, True armour 55%... So it depends on the skill of the enchanter \:\) To have all runes and fortification and true armour would need... upwards of 300% enchantment skill? \:\)