I'm not an expert in this but I think it's probably due to the fact MySQL enforces a maximum key length for indexes. For InnoDB this is 3500 bytes (further limited to 3072 bytes by MySQL itself), and for MYISAM it's 1000 bytes.
Whether or not the value columns are indexed is actually done on a per field-type basis. For example, the long text field type (for fields like the node body) has no index on the
fieldname_value column, but it does have an index on the
fieldname_format column is a
varchar limited to 255 characters, and so would not produce an index key that is too long. Conversely the
fieldname_value column is a
longtext type, which has the potential to create a key that would be too long. (You can specify a prefix length to get around this but I don't think Drupal supports it).
As another example, if you then look at a table for an
file) field type you'll notice there is an index on the
fieldname_fid column. Because this field is an integer type it naturally lends itself to be indexed, without having to worry about the maximum index key length.
I think it basically comes down to the type of data the field is storing.
bundle/etc. are all integer columns and so can be easily indexed by whatever storage engine you're using, while
text types (or
varchar types with a large enough length) will create an index key that's too large for the storage engine to handle.
Hope that helps a bit