The alignment-dependent ionization of acetylene and ethylene in short laser pulses is investigated in the framework of the time-dependent density-functional theory coupled with Ehrenfest dynamics. The molecular alignment is found to have a substantial effect on the total ionization. Bond stretching is shown to cause an increase of the ionization efficiency, i.e., enhanced ionization, in qualitative agreement with previous theoretical investigations. It is also demonstrated that the enhanced ionization mechanism greatly enhances the ionization from the inner valence orbitals, and the ionization of the inner orbitals is primarily due to their extended weakly bound density tails.