For restoration, I always defer to Tom Johnson's practice (Thomas Johnson Antique Restoration on YT) when in doubt.
Unless the dowels (or tenons) are in poor condition, loose fit if not replaced, out of round, or the old glue cannot be properly removed, I'd prefer to keep and use the original dowels for two main reasons: 1) maintaining the authenticity 2) avoiding unnecessary work (e.g. removing or drilling out the old dowels).
If you clean a dowel hole and result in a bigger hole, you may need to redrill the hole and plug it -- which is more work. So be careful when cleaning the dowel holes for glue residue.
The same applies to screws and hardware as keeping the original character (sometimes, including minor blemishes) is desirable or important for an antique piece. Use the original materials where possible unless they would result in a weaker structure or strength.
For restoring antique pieces, consider using Old Brown Glue or the like, which would make future restoration effort (e.g. 50 years later

) easier instead of yellow glue. However, don't shy from using yellow glue or even epoxy glue or new wood if that's the right glue or material to use for a fix.