Hi Babak and Johannes and thanks for your posts. Also sorry for my late response, but here we go:
RESULTS’ FILE SIZE
As it’s easy to guess I already deleted it 
I don’t know what went wrong, but ultimately decided to stick with manual determination each time (total run time divided by time step).
You may be right and all meshes, pre-processor definition files and results files could just pile up together as I keep it all in one project directory. On the other hand, using manual approach I’ve never encountered such situation. I’ll let you know if I hit it one more time.
ACCURACY
I’m happy with regular underestimation. As you mentioned simulation doesn’t include elements such mud, underwater current, random dirt and scratches on hull surfaces etc. - hence the scatter in experimental outcomes and nearly 10% measurement accuracy.
Two curious details:
- vehicle’s handlings alone (the two rings at the top of the ROV) increase the total drag by about 10% in comparison to the vehicle without them
- the grill increases the total drag by 45-50 %.
BOUNDARY LAYER and Y+
Yet again I see we understand each other very well. I also think mesh and Boundary Layer in particular is the region where I should look for any gains. I know the mesh is imperfect (I run separate topic with it here Taming relative meshing | snappyHexMesh ), but I encountered similar problems in other software too. – BTW I think it’s a very good example of difference between solving theoretical and real problems. In real problems often something unexpected causes big troubles and compromises final solution.
Generally speaking it’s very difficult to meet Y+ requirements in some regions - for instance the handlings. These two rings need really dense mesh to map the surfaces properly and at the same time are so small that, inside their geometry, they can hardly contain required BL.
This is the reason why I had to turn the blind eye at some regions and why I decided to publish the outcomes despite all this imperfections. My judgement was based on results repeatability for different mesh settings.
Of course I still believe we’ll find some solution and / or explanation for mesher behaviour.
In terms of Y+ values for particular cases they are up to:
ROV SP+G: 210
ROV SP: 180
ROV WJ50: 250
I’ve run the simulations with a use of SST model, so reference range is 20-200 (or 30-300 as some may say). If we look at the theory the transition point for wall function in this model is at value 11.28 (or 11.68 I can’t remember this precisely). Anyway it’s easy to remember the number is flat 12. For safety reasons we move it up to at least 20.
The upper limit, theoretically, doesn’t exist, but operating with thousands or more – from my experience – can be deceptive and it’s better to keep values at hundreds range.
In my cases the overall layouts are not perfect (due to reasons mentioned in separate topic), but they still look ok(ish). Of course the regions with very high refinement (e.g. bended corners) go below 12, but I’m afraid I have no choice but accept it.
MESH COUNT
Mesh count here is much higher than I expected. But I think it’s all due to cut-cell mesh. A kind of price you have to pay for its regularity. The reference count for mesh elements was about 2.5 million and for nodes up to 1 million. What we have above is:
ROV SP+G: ~13.9 mln elements and ~5.17 mln nodes
ROV SP: ~7.75 mln elements and ~2.9 mln nodes
ROV WJ50: ~9.15 mln elements and ~3.5 mln nodes
Personally I wouldn’t complaint about it. At some areas the mesh may look a bit too dense, but on the other hand it’s nice and regular. I see it this way: in 2D tetramesh when you want to coarsen or refine your mesh you just add an element a bit deformed in comparison to the previous one (slightly bigger or smaller). And you can control step size too. In cut-cell however the step is always ‘2’ (or 100% if you prefer this labelling). Anyway I prefer this approach even if simulation lasts longer.
ABSOLUTE TOLERANCE
(My account yet again switched to free mode and at the moment I can’t do anything, but as soon as Agatha fix it 
) I’ll experiment with the settings more and let you know if and what influence on residuals it has.