Cargo and transit pax, especially to Australia. There are lots and lots of Maltese emmigrants in Australia, IIRC there's actually more Maltese/people of Maltese descent living in Australia than there is in Malta. In fact SQ used to fly SYD-SIN-MLA-AMS back in the days with B742s.

Basically EK is the most convenient airline out of MLA to anywhere east of Malta as they offer great connections and cheap-ish fares. The other options for long-haul travel is either with BA which isn't even a mainline service as MLA is served by GB Airways and is a hassle to connect, having to transfer from LGW to LHR v.v. Then there's LH but only good for trans-atlantic since most of their Asian arrivals does not allow for same day connecting services via FRA. However this should change since KM and LH have signed an agreement to increase traffic via MUC. The remaining airline is AZ which is a bit of a joke since they are notorious for strikes, in fact I think there was one just yesterday. Previous to that SR was a very good airline out of MLA, too bad they went under.

Finally an incentive for EK to fly to Malta is that they have traffic rights on the LCA-MLA-LCA segment since it is flown in codeshare with KM, kind of like the agreement EY has with SN over the BRU-YYZ-BRU sector.