An ambidextrous Character gets -10 instead of -40 when attacking with an additional weapon.

The Hari no Okina (Three-section Glaive) is a two-handed weapon that gives you an extra attack as if attacking with an additional weapon, but at only a -10 penalty instead of a - 40.

Do they stack? and if so how? no penalty? -5 penalty? which one would you pick for a house-rule?

Any answers would be much appreciated.

Based on what you've said here, I would say that the effects don't stack. (so an ambidextrous person wouldn't feel the special effect of that weapon, wielding it with -10 for an extra attack seems just as natural as anything else)