Yes they probably can see them.
Due to their classification as XXXX, only experienced wizards (or Hagrid) should try to handle Thestrals. Breeding as well as owning these beasts may be discouraged or even illegal without Ministry consent; in fact, wizards that live in areas not protected against Muggles are forced by law to perform Disillusionment Charms on their Thestrals regularly.
From FBAWTFT pg 42
.."and the rare Thestral(black, possesed of the power of invisiblity, and considered unlucky by many wizards). As with the Hippogriff, the owner of a winged horse is required to perform a Disillusionment Charm upon it at regular intervals....
Also, read the M.OM. Classifications on pg.xxii A winged horse has a classification of xx-xxxx
xx Harmless/may be domesticated
xxx Competent wizard should cope
xxxx Dangerous/ requires specialist knowledge/ skilled wizard may handle
This is just to understand the classes. A winged horse is a Thestral and why would a charm be needed if muggles can't see them.