You don't have to think twice about doing MA in History from IGNOU through distance education mode. The certificate you get after passing out has value and is considered equal to the regular study. Nowhere in the certificate, it will be mentioned as distance education. The advantage of attending regular classes is that you have a tutor to teach you and you have friends and you have the whole atmosphere to study. Whenever doubts arise, you can check with the teacher or consult with classmates. When you are doing distance education through any centers or institutes, still you have the opportunities for all the above. But if you are intending to do self-study, try to arrange a tutor for the difficult subject or so. If you are able to manage it yourself well and good.
With regards to applying and appearing for NET, you can definitely apply for it with the MA History qualification from IGNOU through distance education. I have done PG through distance education from Calicut University and have appeared for NET exam. You can appear for NET during your last year of PG itself, and even if you clear NET, you have time to submit your documents which includes the PG certificate. It is better to appear for NET while doing PG itself, as you will be fresh and you have a clear idea of what you are studying. If you appear for NET after PG, then you might not recollect all the things you learned and will have to study from scratch.
To conclude, don't be doubtful and waste your time and years. Register for MA History with IGNOU (Distance Education)and start studying. Meanwhile prepare for NET as well
"Do not give up, things might not favour you always"