There are three places that losses can change when you adjust the system under some assumption of "constant load" (which I interpret as constant total fluid horsepower of driven machines).
1 - Motor - adding an identical motor with the total bhp of 3 motors remaining the same has somewhat unknown effect. The total I^2*R losses will likely go down (because each motor carries less current, and the I^2 part tends to dominate... if all 3 motors had for example 3/4 of original curent, each motor would have 9/19 of original I^2*R, and the ratio of new/old total I^2*R would be [3*(9/16)] / [2*1] = 84% (a reduction). What would increase is the total core and friction/windage losses. Which one wins of these two opposite effects would require some careful study.
2 - VFD. We have similar situation: the total load-related I^2*R losses will decrease, but there are other losses where the total increases. I'll take Jeff's word there are likely more losses in three vfd's operated at 66.6% than two vfd's operated at 100%
3 - Load - completely unknown to us. Often driven loads operate at much lower efficiencies than the motor that drives them and changes in efficiency of load under different operating conditions can be huge.
Whether #3 will counter #1 and #2 seems to me difficult to predict. I do certainly agree with jraef and davidbeach that a lot more data would be required to draw any useful conclusions.
Adding a 3rd machine and associated vfd is an expense. Aside from any change in efficiency, I'd think it generally tends to increase your reliability and flexibility (for example if 2 machines carry 100% load, then we can stay at 100% load even if one machine stops or is taken down for maintenance).
So, more info about the loads. What type are they and how are they interconnected. If possible what would be the driven machine efficiencies when operating at 44hz and 26hz and carrying the respective expected load (efficiency depends on fluid load and speed). And how did you determine that 3 machines at 26 hz would "carry the same load" as 2 machines at 44hz for this system?