Thanks to Fitzcarraldo i got answer to my question.
Indeed, in the Traveller v2.6 TMO mod the submarine's crew earned XP points slower than in TMO 2.5 - just as i thought.
Meantime i will disable Traveller v2.6 TMO and return to my previous mod list which worked perfectly throughout many career patrols.
The Traveller v2.6 TMO mod has many great features, but unfortunately is quite unstable and incompatible with other mods that i like (i.e. OTC 1.5).
I will try to implement some Traveller v2.6 TMO mod features into TMO 2.5 and RSRDC campaign.