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You cannot do this automatically yet, but if you go for the 'find users' option in your admin panel, you can find all users that have last logged in more than X days ago. So if you wish to delete all this users you can simply select them and delete them.

I am keeping silent on the fact that this would seem to be very rude to users, to delete then without warning or notification . They would probably never register on the site again, even if they like your site but simply dit not log in for some time.

I'd simply alter the welcome e-mail to say that if they don't login at least once every 6 months that their account will be deleted to make room in the database. I think once every 6 months is not asking too much.

That is of course a possibility . If you have a database of 100.000 users and you delete 30.000 users this may have a very minor effect on the speed of the site. Anyway, the possibilities to manage this manually are there, but an automated management tool might be handy in the future.