What happens about those mods and the special kernel when a software update is needed?

... no answers ? :(

I think that with custom kernel, there is some mean to "lock" it to avoid losing mods and so on...

for other things I do not know, but it seems that also for this reasons, future versions of Niceeepc will take form of .deb packages to install, remove and update using the package manager.....

1) overclocking : cat /proc/cpuinfo gave me 675 MHz in overclock mode and 630 in normal mode, it's normal? (won't be 900 instead?)

Yes, that's totally normal, check:
http://wiki.eeeuser.com/howto:overclockfsb?s=overclocking

"N.B.: It is common practice to check the speed of a CPU by “cat /proc/cpuinfo”. In this case, that procedure will not work; /proc/cpuinfo will always report 630 MHz, even though the system may in reality be at 900 MHz. The only way to verify 900 MHz (or any speed different than 630 MHz) is to do some benchmarking."

To do benchmarking you can use glxgears with and without overclock.

2) About software upgrades: here in my fresh ubuntu hardy 8.04 I need to upgrade, but... what happens to all the scripts, tweaks and to the special EEEPC kernel here? will they be overwritten by the upgrade?

Upgrades are relevant only when you upgrade the Kernel. It depends, if you choose to install special modules over the vanilla kernel NiceeePC will detect the update and recompile everything for you. I it doesn't, you can always type:
niceeepc manual
kernel_upgrade

Or in v1.3:

niceeepc manual kernel_upgrade

NOTE: If you have 1.0 and custom kernel you should never run this command. In 1.3 it's impossible.

To upgrade every kernel related fix.

If you choose Custom Kernel you should never had any problem at all. There is a bug, already fixed in 1.3, that in previous version the system could update from custom kernel to vanilla kernel.

About 1.3, is already finished. You can download the code at launchpad. I haven't made the official release because I haven't tested it from top to bottom. For this is I need to reinstall Ubuntu in my eeePC, but I'm using it right now and in production. Maybe this weekend, but I can't be sure.

Cheers.

"I think that with custom kernel, there is some mean to "lock" it to avoid losing mods and so on..."

Yes, this is already applied in 1.3. I'll be releasing it soon, I promise.