If you're careful not to get it too hot while drilling and sanding, the smell should disappear in a couple hours. If you do heat it up, and you'll know by the smell, it will continue to outgas for a few days.
Also, while drilling, I've found that SHARP twist drills with 90 degree points are best. A dull bit will just scrape and abrade the material away - resulting in lots of heat and lots of lingering smell. This is especially important for big holes. Along the same lines, I've found that spur point bits are not suited to ebonite, since they end up scuffing and overheating the ebonite on the hole wall.
I only finish ebonite (both on pens and pipes) with Abralon up to 2000, a buffing with brown tripoli, a buff with white diamond, and then a quick buff with plain carnuba wax.