[SalesForce] Convert Lead to Opportunity via data loader

Yes, it's possible to mass convert leads in Apex Code. See the documentation on Database.convertLead here: Database.convertLead docs

You can convert up to 100 leads at a time and you can use it in a scheduled class or as part of a batch apex operation (or both) if you want to convert much larger sets of leads. The documentation linked above contains good sample code at the bottom of the page. However, the example is for a single lead, here's a multiple lead conversion example:

// Create some sample leads.
List<Lead> myLeads = new List<Lead>{
    new Lead( LastName = 'Last1', Company='Company1' ),
    new Lead( LastName = 'Last2', Company='Company2' )
};
insert myLeads;

// Get a valid lead conversion status.
LeadStatus convertStatus = [SELECT Id, MasterLabel
    FROM LeadStatus WHERE IsConverted=true LIMIT 1];

// Create a list of lead conversions, then create a leadConvert object
// and add it to the list of lead conversions to be executed.
List<Database.LeadConvert> leadConversions = new List<Database.LeadConvert>();
Database.LeadConvert lc = new database.LeadConvert();
lc.setLeadId( myLeads[0].id );
lc.setConvertedStatus( convertStatus.MasterLabel );
leadConversions.add( lc );

// Create the second lead conversion and add it to the list.
lc = new database.LeadConvert();
lc.setLeadId( myLeads[1].id );
lc.setConvertedStatus( convertStatus.MasterLabel );
leadConversions.add( lc );

// Execute the conversions and check for success.
List<Database.LeadConvertResult> results = Database.convertLead( leadConversions );
System.assert(results[0].isSuccess());
System.assert(results[1].isSuccess());

I haven't tried this, but according to this site: http://www.interactiveties.com/b_bulk_api_nulls.php

If you use blank values (not #N/A) for the fields in the spread sheet pertaining to updates, then the fields should not get updated for the update records.

If you use this in conjunction with an upsert based on either the id or an external id, then that should help you out.