Shield mitigation and armor. The thing you have to understand about Sins is that almost nothing deals close to its potential damage output in practice. Less than 20% of total damage is totally possible and even normal.

Shield mitigation is by far the most important one. As units take damage their shields get better at reducing damage, and this effect works even if the shields are "down". Even frigates can get mitigation values as high as 57%. Capitalships and titans could in theory get above 80%. 80% shield mitigation alone would reduce 5000 damage to 1000 damage, not including other buffs like damage reduction or sharing that might be in effect.

Armor is not as important because it basically acts as an increase to maximum hull, though it also contributes to hull damage not receiving the damage on the info card.

And to be clear, this affects almost all damage in the game, save sometimes phase missiles and hull draining effects like Nano Disassembler. Your base weapon damage will also be reduced by the same amount, so no your base weapons are not doing any more damage (as while the Coronata actually has the highest base damage of any titan, this is because it can target many ships at once, Unity Mass is what gives it its strong single target hitting power).

What you're observing isn't unique to unity Mass.

Against capitalships in long fight, pretty much all damage is mitigated by 65-88% before being dealt to the target ship.  The main causes are:

1). Shield mitigation- as ships take damage their shield mitigation rises(you can see it's current value on the infocard).  Capitalships can generally have a shield mitigation of 70% or higher.  70% shield mitigation means they only actually take 30% of incoming damage- less the one third

2). Armor-  Any damage dealt to hull is reduced by armor.  Expect a 17-33% reduction in damage by armor from capitalships in most cases

3). Ability damage is reduced against capitalships-  All ability damage is reduced right off the bat by 25% when applied to capitalships.  Capitalships are just somewhat resistant to ability damage.

ALl this together means observing 1/5 damage is pretty normal.  And it's not just unity Mass, this is true of every ability in the game- and besides #3 is true of ALL damage, including autoattack damage.  Unity Mass is a very strong skill- a potential 8750 pre-mitigation damage is a lot.

Also keep in mind Unity Mass can do a lot more damage if you use it as an opening shot on a ship that has not taken any damage yet(and thus only has a shield mitigation of 17-20%).  That said, it takes VERY little damage to cap out shield mitigation, so the only way to really accomplish this is to manually make sure NONE of your ships attack the target before the first Unity Mass.  The rewards are worth it though, as in this manner you can easily score 2500-4000 damage Unity Mass shots.

Unity Mass has become quite powerful with the latest patch.

Especially in combination with Suppression Aura. The Aura makes it nearly impossible for any capitalship to flee and Unity Mass will tear them apart. Its powerful enough to hurt even enemy titans.... who are suffering under Suppression Aura at the same time.