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What's the difference between M.Tech(IT) from IIIT Banglore and M.Tech(CSE) from IIIT Delhi?

Is this (being IT and not CSE) the reason for lower cutoffs for IIIT-B and does this has any affect on placements?

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Delhi.

Reasons:

1) Higher research output by professors.

According to csrankings.org  IIIT Delhi ranks 26 in Asia and Bangalore ranks 46.

You can also walk through faculty profiles and their research papers on google scholar to confirm this.

2) All MTechs get stipend in Delhi. AFAIK only top 50 get stipend in Bangalore

3) Placements are more or less comparable but Delhi is slightly ahead.

Median CTC Delhi: 14 lpa

Median CTC Bangalore: 11 lpa

4) Ok this point isn't really that strong but a CSE degree always sounds nicer than an IT one. You won't face any problem due to your Degree's name though. No one cares about this.

It is important to remember though that both of the institutes are excellent and no matter which choice you make, you will have a good future provided you work hard and make best use of your time.

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