yes, there are rubber plugs all over, these are from painting the body of the car in the factory. The body is 'diving' thru a paint and after it leaves the remaining paint drains thru these holes.
Sometimes these rubber plugs come off, for example pushed out by a wrong placed lifting tool, then this is a 'nice' ground for rust.
The plugs you can get from dealer, see www.realoem.com
Here some pics from my parts car E32 where you can see the holes
http://www.bimmerboard.com/forums/posts/270025/