If i attack using a character with STR 4 and intimidate and then declare a naval attacker of STR 3, obviously intimidate means the str 3 character doesnt count his strength but does he still count to have participated for the purpose of black sails etc? I would have thought so but wanted to check.

Yes, a character is still participating in a challenge even if his strength doesn't count. This works for Black Sails, but also renown or deadly.

and stealth, and relevent abilities (thinking of one Iron Fleet Captain, whom I adore with Long Ship Grief and bulky intimidate raiders such as Euron's Enforcers)