National Electrical Code simply states that all openings must be closed. An unused breaker or cover likely both meet that requirement, so either should be fine.

I don't think there's a rule that says "Thou shalt not leave unused breakers in thine panel.". But I could be mistaken.

Remove and discard the bad breaker.

National Electrical Code 2014

Chapter 4 Equipment for General Use

Article 408 Switchboards, Switchgear, and Panelboards

408.7 Unused Openings. Unused openings for circuit breakers and switches shall be closed using identified closures, or other approved means that provide protection substantially equivalent to the wall of the enclosure.

^{It's possible that the AHJ could argue that a breaker does not meet this requirement, but that would be completely dependent on the opinion of the individual.}

To answer your biggest question: I'm pretty sure it's not code-legal to tap into the feed from your meter panel with split-bolt connections. It's possible that your breaker panel has some lugs near the bottom of the load side bus bars to connect a feed to a subpanel, but most don't.

So a possible solution is what Doxy suggests: a new 100A panel that feeds your existing panel as a sub-panel. Before you consider that, I'd check to see if your panel type admits half-size tandem breakers. These are breakers that fit two half-size breakers into the space for one normal breaker, and this would free enough space for a 40A breaker to your EV charging circuit in the garage.

Another possible difficulty, though, is that your 100A service is awfully marginal for the addition for a 40A EV charging circuit. Although you didn't give all the relevant details, I assume your 1000 sq ft house (does this include the basement, if there is one?) has an electric dryer. In my jurisdiction, a load calculation shows you would require a 107A service. You may be able to get away with a 100A service, but it will depend on your inspector/permitting authority.