While we don't know for sure yet since the only other thing that's negated "secondary effects" besides Stoke is Shield Dust, which only negates secondary effects to you caused by the opponent, it's safe to assume "secondary effects" is more like chances for burns, freezes, paralyzes, flinches, sleeps, poisons, and maybe even stat debuffs from your attacks on the opponent like, say Mud Slap's accuracy drop or more likely, say, something like Psychic's chance for a Special Defense drop. I don't think it'll work on self-inflicted stat debuffs like Close Combat's attack and defense drops or recoil, which I honestly don't think is technically a "secondary effect" at all, contrary to what something like Serebii's attackdex might call it.
Assuming Hihidharma gets Flare Blitz, though, it'll still get a boost since Flare Blitz has a chance for Burn. Can't think of anything particularly useful Stoke can boost for Wargle. I guess maybe Air Slash if it turns out to be mixed or Special oriented.