The power generated during turbine operation is calculated as:
Where (H) is effective head is the head which works effectively for the turbine, and expressed as follows.
H = Hg - Hl
Hg is gross head and for reaction turbine (such as Franacis & kaplan) it is between Dam reservoir level and tailrace tunnel outfall tail water level and in case of impulse (Pelton wheel) it is head between reservoir level and nozzle level at turbine location in power house.
Now Hl is head loss in water conductor system which depend upon various factor such as friction loss in water conductor system, bend loss, entrance loss, exit loss, transition loss, gate loss etc.
η is the product of all of the component efficiencies, which are normally the turbine and generator.
As you pointed out nowadays Francis turbines has a very high degree of efficiency of more than 96 % and Kaplan turbines have 95 %.
But in addition to that generator efficiency also contribute in overall efficiency . Typical values for generator efficiency range from 91 to 98%.
Say if turbine efficiency is 95 % and generator efficiency is 95 % than overall efficiency becomes = 0.95*0.95 = 0.9025 or 90.25 %
The losses in water conductor system varies w.r.t water conductor system and its project specific. For longer WCS the losses may be high.
The total head loss varies and is project specific but for clarification based on my project experience it might be in the range between (4-8) % ( note:- this might varies and mentioned only for clarification) .
So say if for any project head loss is 5% of the maximum gross head at maximum discharge than effective head will be 95 % of gross head.