Digging out the report I see Aldebaran was recorded at 45 deg altitude
I dont think scintillation effects are directional are they ? I would expect the effect to be independent of the slit orientation. Orientating the slit vertically relative to the horizon (the paralactic angle) will help with atmospheric dispersion problems though which can give systematic errors due to selective sampling by wavelength at the slit.
EDIT: Actually thinking about it a bit more, I think there are two potential effects here.
Movement of the star image coupled with selective sampling at the slit due to atmospheric dispersion which could be reduced by orientating the slit
Distortion of the spectrum due to scintillation which is seen even in the absence of the slit (eg in Star Analyser spectra) and is seen visually as apparent colour changes in the star