The secondary modes of weapons can actually be thought of as completely separate weapons. The executioner sword has a one-handed secondary mode so for all intents and purposes it is a one-hander in secondary mode; no penalties. Also, there was a patch a long time ago that removed the damage penalty for two-handers used with a shield, so even if it was one of those two-handers it would still do full damage.
Coincidentally this also affects the damage of two-handers used from horseback. So any two-hander that is usable with a shield does full damage from horseback (still gets a speed penalty though). For this reason I'm kinda surprised that I haven't seen more mounted Persian battle axes.