Having looked through that conversation, the £1000 he referred to was definitely the bond repayment over and above his salary, not that he was paying a grand out of his salary.
Because of likely repayment structure, there shouldn't really be any impact on salary until you've already taken a couple of steps up the pay scale. It would also depend on the size of any loan being repaid and the interest being applied to it. This will vary from cadet to cadet. Not that anyone should be divulging the specifics of their particular arrangement, the agreements are confidential and specific.