Supposedly, if it works like adventure mode, the cap is either double the dwarf's start / base value, or the base + 1000. So if the base is below 1000, its cap is going to be lower.
It's base + racial average.
I'm actually not sure if this does work the same as adventure mode, because I've seen some dwarves with absurdly high physical stats after years of training, which would have meant starting attributes near 1500. It's possible I believe, but pretty unlikely.
Depends on the stat. A starting Agility of 1500 is rare because of the 900 average, but 1500 starting Strength or Toughness is more common because of the 1250 average.
What stats were you checking for? It's possible it's one that a danger room doesn't train?
Danger room stats depend on the skill being raised.
Weapon / Shield: Agility, Kinesthetic Sense, Spatial Sense, Strength, Toughness, Willpower
Armour: Endurance, Kinesthetic Sense, Strength, Toughness, Willpower
Dodge: Agility, Endurance, Spatial Sense, Toughness, Willpower
Assuming the wiki is correct on this, it's possible to miss out on Endurance training if your dwarves use parrying and shield blocking exclusively. The wiki doesn't state how much each stat is raised by a skill, and it may be that some stats are raised only enough to maintain them.