I think Lakshadweep is a preferred target for those resigned to take their honeymoon within India's borders. We had a half-hearted plan to visit some years back (not as honeymooners ), but got put off by the requirement to get special permission. Tiresome though not insurmountable, but life's too short..

I think Andaman is unlikely to have the same attraction for Indian newly-weds, and some form of protected area permits are required, with certainly a more serious version of PAP for the remoter islands. The murder of an American missionary on one of those remote islands a few years' back is unlikely to encourage tourism: and for their own reasons, the indian government is perferctly happy with that status quo.