I use in my Recherche bilateral import data (between two countries). How can I distinguish between zero trade value and just unavailable observation?  

In general, countries send data to UN Comtrade in full breakdown of partners and detailed commodities.

 To spot unavailable data, you can check data availability. UN Comtrade data availability is based on combination of Reporter, Year and Classification. By going to this page http://comtrade.un.org/db/mr/daYearsNewResults.aspx?nom=all&px=ori, you can download all available data availability since 1962. If you make a query, also make double check with the data availability list. 

Zero trade value may be more difficult to spot due to confidentiality and due to mistake during data compilation or processing. You should check the trade from/to between those countries.