Mine have the rigid boot, not the accordian style, and had no drain holes.
The reason I mounted them upside down is D: None of the above. I had the same reasoning ChuckH mentioned, to prevent crud from accumulating in the little dished area on "top" of the can and being worked into into the can. Not likely stuff would get there under street use, but I don't think Bilstein expects them to get many dunkings in funky water. Reducing unsprung weight is a plus I suppose, but not a consideration.
I figure that even though I can't invert the front shocks, they're a bit less likely to see the nastier water since they're not going to see much of the crap the front end stirs up.
Brent