There's not a definitive answer for your question. If you're trading items across accounts with an account used for botting, then yes, both accounts can be flagged. Will it happen? There's no answer to that. It very well may be dependent on the Blizz rep that reviews your account.
And if you want a secondary account on your main account, recruit your email through the Recruit-A-Friend and start the account that way. That way, if you do play the accounts together, you'll get all the recruit-a-friend benefits.