yes and no.

it is generally always good to mask the repeats in (new) genomes. Don't remove them though! but rather soft (or hard) mask them.

On the other hand, those repeats should not interfere much with phylogenomics analyses, as those kind of studies are primarily based on 'normal' protein coding genes. In that sense it is important to make sure the repeat(proteins) do not end up in your proteome for a certain organism.