Broker deposit bonuses can affect automated trading calculations if the software considers the bonus as part of the account equity. This can lead to miscalculations in risk management, resulting in higher-than-intended risk per trade. For example, if you intend to risk 1% of your account balance on a trade, but the software includes the deposit bonus in the balance, you might end up risking 1.2% instead. It's crucial to ensure that any trade assistant or copier you use does not factor in the deposit bonus when calculating risk, to avoid over-risking.