It doesn't matter if you enter them or not, it will not cause any issues when traveling. This might not hold true for VISAs or mismatching VISA details (i.e. your doesn't have the middle names).
In thousands of flights I've never entered my middle names on any passport detail page and with the exception of some Asian countries (years ago) it has never been issue. It wasn't an issue there either, the ground staff just added them to the system.