I mean in Inkscape when you save it doesent ask you if you wnt to overwrite the file, but Blender does, so
What is the best way to go ?
What do you think ?
I certanly dont know, in Blender i am used to non modal(asking)
but in inkscape i just ctr+s and i save directly.
What you think ? 
Blender’s approach is better for working with complex 3d. In simple apps like open office, inkscape, and even Wings3d, saving in-place makes sense because you can be confident that everything you’ve done to that point was either revertable or what you wanted. They are small-scale apps that are not powerful enough to wreak havoc.
However, if you’re using Blender, hopefully you’re taking advantage of its advanced capabilities: multiple objects, materials, animation tracks, particles, cameras, and so on. This means that you can easily introduce a subtle error into your file, and not notice it until you’ve saved right over it! And in 3d, a subtle error in one place can screw up a lot of stuff. Working with nodes, topology, and tweaky things like particle systems REQURES a save to be non-destructive. If I were winging it on a topology puzzle, and pressed ctrl-W instead of ctrl-E, save-in-place would be horrifying.
So while I like the save-in-place of simple apps, for powerful 3d I prefer confirmation, and above that the automatic versioning of blender. It has already rescued me from hours of retooling.
If there’s two things that people want a confirmation for it’s saving and quitting. The developers could put the confirmation in the status bar at the top, and not have it save or do anything untill the user selects ‘yes’ or ‘no’
I saw a little thing in the mailing list suggesting they could put a ‘what happened’ thing to get rid of the popups, when you merge or remove doubles for instance.