It Depends, it depends
It depends on how you use your batteries.
Two 6 volts in series and a 12 v starting battery where all are of the same type (wet cell not mixed with gel or agm) should work fine since the charging voltages for all three batteries would be the same.
That set-up is fairly common with cruising sailors and works well. In fact, If I recall Practical Sailor had a study some years ago and determined that golf cart batteries (6V type) worked out to be the cheapest over the life of the batteries and they considered all types.
I'm not sure Trojan 6v work out to be the cheapest although they have a good reputation for longevity. Last time I looked you could get 6v golf cart batteries at Sam's Club for about $42 each which makes them really cheap.
The issue from a cruiser's point of view, is that wet cells of either 6v or 12v varieties require attention to maintenance, i.e. watching electrolyte levels and charging cycles. If you fail to maintain them properly, you won't get the life out of them.
It really shouldn't matter whether you use 12v batteries or 6v batteries. The only difference between them is the number of cells. 6v batteries have 3 cells (about 2.12v each) in series. 12v batteries have 6 cells (also about 2.12v per cell) in series. Two batteries in series (6v) or two batteries in parallel (12v) get you the same total amp hours and take up the same amount of space (approximately).
The maintenance amounts to making sure the fluid levels are correct and that the charge - discharge cycles are appropriate for wet cells.
One major maintenance issue with wet cells is that the outgassing, caused by charging, depletes electrolyte and it also causes a caustic gas that tends to corrode terminals. Not to mention that the gas (hydrogen) is pretty explosive stuff although lighter than air.
Never let the fluid level get below the top of the plates, keep the terminals clean and never discharge below 50% before recharging and the batteries will last for 5 or 6 years or maybe longer with the Trojans.
On the other hand, if you occasionally abuse your batteries, like I do ... i.e. discharge below 50%, tend to forget to check the fluid, never clean the terminals, require fast recharge, depend on solar cells, use minimal recharge cycles, etc ... you'd be better off with AGM or Gel batteries.
Just my HO.