Anirban, Peanuts boiled in the shell are nutritionally superior to boiling shelled peanuts, but it is fine to boil either type of raw peanuts.
The shells do seem to provide some additional nutrition, but boiled peanuts themselves are full of nutrition whether they are boiled boiled with or without the shell.
Peanuts will boil quicker when they are not inside the shell. As always, taste samples often to decide their softness. The peanuts must soften before the salt water can infuse the boiled peanuts.