1. Will such a change require clients to have a modded version as well,
or will calculations like that reside with the server? (Since no block
id's and such are changed I figured it might be possible)
I think only Serverside.
2: Am I allowed to do that on a server other people can access, or have the creators of IC forbidden modifications?
Not directly forbidden. You just cant decompile/recompile IC² correctly without hacking the Sourcecode.
The change itself for the flowing Water is easy, but Limiting EU/t even more is not recommended (roundingerrors making it 0)
public void updateWaterCount() {
...
if (this.worldObj.getBlockId(var2, var3, var4) == Block.waterMoving.blockID || this.worldObj.getBlockId(var2, var3, var4) == Block.waterStill.blockID)
...
}