Yeah, ditto. If you think they are small enough to sew and close the hole in a way that is also cosmetically acceptable to you, then do that with a few stitches, and seal it on the inside with some mcnett seam grip. This will be waterproof, but it should also bind everything together and prevent further enlargement of the hole.
If the holes are larger you can do the full monte and use a patch with this same technique.
I think you can safely use standard polyester thread.