Hi Sarbesh, there is usually at least some bias in any cloning method. For BAC clones, using sheared DNA rather than restriction enzyme cutting helps. Even in this case there is some bias which can even be a function of the insert sizes.  For a theoretical treatment you can look at Genome Res. 2001 Feb; 11(2): 274–280., For a real world example  Genomics 89 (2007) 291–299.

Good Luck

I would expect for most purposes this would "evenly" cover the genome. Of course, whether this is "representative" is another question. genomes are not uniform (in terms of GC, gene density, repeats), so without the rest of the genome it may be difficult to put it in any useful context. Even individual chromosomes are not uniform (such as human http://www.ncbi.nlm.nih.gov/pubmed/10830953).

In my experience, not only the repetitive regions are more represented than the low copy regions, but also some regions are more represented than others, just by chance and depending on the cloning technique used. If you select only clones that contain low copy regions, they should represent better all of the non-redundant regions.