Weapon skill effects damage and hit chances, as well as parry chances. I don't want to post any equations since they are subject to change.
I think counterstrike chance is determined by your general skill amount, the same thing that gives you attributes. Part of the Combat Arc is to handle this more properly.
Yeah, shield skill should increase your bashing effectiveness with a shield.
Armor skill decreases the effective weight of armor in your inventory (both its effect on speed and attack rolls) and gives a chance to increase the blocking power against attacks.
Ambushing increases your chance of remaining undetected as you attempt to sneak and attack, but sneaking is very crappy right now, so it's hard to notice sometimes.
Yeah, fortress skills do that.
Agility governs many combat rolls and your maximum speed (though the speed system is weak now and should at least be divided into movement and attack speeds, outrunning lions by having one agility level is dumb).
Strength increases melee damage and the amount you can carry before your become slower and less able to strike.
Toughness increases damage resistance, improved exhaustion checks, stamina recovery rate, speed when parts are broken, time you can go without air and pain tolerance.
A lot of these might be fleshed out/separated a bit, and increases won't be linked to total skill gained so much in the future. As you can do more in the game, other more mental attributes can be included, but they just... aren't important yet.