Your legs will atrophy with that change in stimulus regardless of how many hindu squats you do.
Bodyweight squats as cardio will be highly stressful on your knees as they track way over the toes when performing a hindu squat. It's not something I would do regularly or for super high reps.
I would suggest kettlebell swings as an alternative that can be done in your living room.
I'm not sure why you got the impression that I'll be doing Hindu squats. My "bodyweight squats" use the same posture as my front squats (without the bar). In any case, I'll give kettlebells another look. Thanks.
Try to predict something important in a way, that it will be easy to judge it in 2014, how (in)accurate your predictions really were. Don't leave too much space for a doubt what was really said.