How is the number of chromosomes determined from a newly sequenced bacteria genome. Can this be verified from the sequence data?
Bacteria (generally) has only one circular chromosome (but can contain multiple plasmids), therefore your sequencing must show only one large contig.
I guess this may be true for many bacteria, but as with many things in biology there are always exceptions. There are bacteria with linear chromosomes and multiple chromosomes (as well as collections of plasmids). See e.g. http://microbewiki.kenyon.edu/index.php/Chromosomes_in_Bacteria:_Are_they_all_single_and_circular%3F#Multiple_Chromosomes and http://micro.cornell.edu/cals/micro/research/labs/angert-lab/genomes.cfm.
To the original question: I think it would be unusual to assess chromosome count from sequence alone. The typical way would be genetic experiments (see papers in the references above) or maybe FISH or PFGE. This isn't my area so I might be very wrong.
In principle, with very high coverage sequencing and long reads, you could assemble the sequencing reads and the number of contigs would equal the number of chromosomes. In practice, of course, repetitive sequence and other problems would break up the chromosomes and you'd have many more contigs than chromosomes.
I agree, biology always comes with exceptions.
The short answer is no. Even a very very good de novo assembly will have more contigs than chromosomes.