If Applejack thought someone was untrustworthy and/or malicious or something like that, but she didn't have any proof, what would she say if someone told her they wanted to be that person's friend?

She'd probably warn them that she doesn't trust the individual in question and maybe that that someone should be careful getting close to them, though not necessarily outright saying they shouldn't try. I don't see why she wouldn't be willing to give her opinion, even if she doesn't have solid evidence, she is the element of honesty after all.

"You want my honest opinion, sugarcube? I don't trust that folk about as far as a line on cider day can be. Somethin' about 'em just doesn't sit right with me."

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"Uh, I don't know nothin' bad about that pony, but-- somethin' about 'im makes mah withers twitch."

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Yes! Spot on, in my opinion!