Hi Roman,
Can you describe the "miscalculation" a little more? Shallow depths should be treated just like any other depth once they are included in a map project. It is possible, however, that you have a number of zero depths that are being excluded automatically during import. If this is the case, you will need to reimport your files and uncheck the "exclude zero depths" option in the import window during the import. This option can be useful to remove bad depth points from tracks, which are very often zero depth. Depths that are non-zero, even by a very small amount, should always be imported.
Matt