MOST definitely and most especially will nokia batts lose their charge if stored and not used.
Even if they are in new unopened packages.

The best way to store li-ion batts is to charge them up to exactly 60% and then put them in a cold / cool storage...at a (the exact temp eludes me for the moment)
ONLY then can it be guaranteed that you will not suffer max charge degradation from the batts sitting idle.
even then..your batts will suffer some loss ..but it will be minuscule.
remember li-ion isn't magic...it is still based on the principles of a chemical reaction to produce an electrical stored charge...and the chemicals in question can and do degrade over time, use / misuse and environmental conditions..
essentially and basically the chemicals are separated by a "barrier" between the two chemicals...and when "used" the chemicals are given the allowance to interact...thus creating the electrical reaction...to add to the issue ...the "barrier" separating the two chemicals can degrade as well...

albeit ..it is an improvement over old archaic batteries...

The only way we can be free of the scourge of battery degradation...
Is alternative energy sources...
say...
to leap technologically to running all our devices off of potato generated electricity...


I wish I could say that the issue lies within the device reading the battery..
But since the issue spans further than simply the n900 and maemo5 os line...and actually encompasses many devices and os's..
I believe the issue is chronic in the battery giving up the proper information to the device.

As far as battery rejuv goes...
I have bought many rejuv'd nokia batts from a supplier here in Canada...they are cheap ...they have a 98% charge max ...they perform for years and perform well ...and they are significantly cheaper than brand new original batts.
I suggest you hunt down a proper professional who does such work...
I lastly suggest you do not attempt batt rejuv without some serious training first by someone who does it professionally..

Of course I am writing all this purely guessing at your possible reply ...not that I have read anything you wrote...