I agree, changing last name now is a big hassle, and will be a hassle till PR gets through. I know of a friend whose wife changed her name halfway through the process. When she got PPR, it was a big problem apparently, and got her file delayed.
Regarding specifying marital status, it is noted in indian passports by the way of specifying spouse's name (in the last page I think, where father and mother are listed too). We did this change as well when we were applying, just because we were advised by family and friends that it will further show that our relationship is genuine. I don't know if it really matters though, but if you do go ahead with it, add another few weeks to the process as a new passport could take at least a couple of weeks.
Regarding specifying marital status, it is noted in indian passports by the way of specifying spouse's name (in the last page I think, where father and mother are listed too). We did this change as well when we were applying, just because we were advised by family and friends that it will further show that our relationship is genuine. I don't know if it really matters though, but if you do go ahead with it, add another few weeks to the process as a new passport could take at least a couple of weeks.