It's very, very negligible. Their cleanliness and overall practicality is more than worth the 1 or two percentage loss in efficiency.
I will never buy a bike without an internal hub gears, ever
I'm glad that there are more choices when it comes to IGH bikes these days.
If you get a fully enclosed chain case, which is admittedly harder to come by, then you will have an almost perpetually new looking chains for the rest of your life.