Yes, including the precursor ion types is a good idea.

The reason that you would want to exclude the small ions is that they are likely not going to be specific to the peptide of interest. Specifically, if you used trypsin to digest your proteins, then nearly all of the y1 ions that you see will just be the amino acid "K" or "R". Therefore, the y1 ion that you see in a DIA MS2 scan might have come from the peptide that you are interested in, but it also could have come from any other peptide whose precursor m/z was within the width of that isolation window.

Note that you can also exclude small ions by setting the Min m/z value on the Transition Settings - Instrument tab to something like 300 (or 250 to 350). I know the Aebersold lab does this in preparing libraries for OpenSWATH, and it may be a more direct way of excluding low m/z ions, since if you allow high enough fragment ion charge states, eventually even larger ions can become low m/z.

Thank you very much.