The 90 dpi comes from a specification and is internally used as based value
Inkscape assumes a 1-to-1 relation at 90dpi (one SVG user unit translates to one bitmap pixel).
For some unknown reason most people assume that webgraphics have to come as 72dpi. This is nonsense, as dpi means nothing on a screen, just the number of pixels are relevant 100x100px will display on a certain size display with a certain set resolution as a real world dimension of n by m cm (or inch or whatever measure of lenght).
Resolution is however important when we want to print our designs on paper. For rasterized images it tells something about how the image was sampled. But for vectors that again means nothing as no sampling is involved (everything is scalable).
So when you make images for web, and you want your image to be 100x100px -> just draw it as 100x100px, export it with the default setting of 90dpi and you get exactly the size you want (a picture of 100x100 pixels - that the dpi is 90 is irrelevant - if you do not believe me: use a program like the freely available
Irfanview and set the dpi to 0 or to 1000 it will still display as 100x100px). So the 72dpi that most webdesigners sorta fix on is irrelevant but it is hard to break habits.
For print however there are different requirements. If I make decorated paper (such as used for photobooks / scrapbooks) it needs to be printable at 12"x12" at 300dpi to have proper quality. I draw my design in Inkscape, do not care about the dimensions to start with (tho I make it a rectangle, and if I would do it properly I would even set up the document to that size- but I am a bit lazy). Then after I complete my work - I do a rubberband selection, lock the ratio in the tool control bar (the little lock between H and W), change the dimension to Inch and set the width to 12 ( height follows automatically). Then when I export my picture as bitmap (png) I tell it to use a dpi of 300. It will automatically recalculate the required number of pixels and set it to 3600x3600 (exactly what I need). So even tho it works internally on 90, you can prepare your export at ANY dpi you want.
If you save a design to EPS, and you try to open it with a image editor like GIMP or Photoshop, it will ask you for the dpi to import the file. As Inkscape uses the internal 90dpi standard, you should say 90 here to get the design over in the same amount of pixels (or multiply/divide with exact numbers to get 50%, 200% and so on), if you change the setting to someting like 72 then the size of the graphic will change in number of pixels and some people are recalculating - doing things like drawing a bit bigger design in Inkscape (125%) so they can import it at 72dpi which they find so important but in real life on the screen means nothing (pixels, only pixels are important).
Now, this is already a long post, but in the same spirit I might as well address the opposite effect too when you import raster images into Inkscape (from the FAQ):
Why do images 'grow' when imported into Inkscape?I hope this clarifies a few things - and just a note - if you deliver true vectors to a printer they can produce it at any size you require without loss of quality. In that case just make sure your document is set up properly.
Cheers,
Syllie