Sometimes we give these things either too much thought or too little. For example, Kira "knocking out" Damar with a blow to the back. A well-aimed blow to the upper spine on a human in that area can potentially kill or paralyze, certainly it could easily put someone out of a fight. Possibly whoever choreographed that scene considered the possibilty that Cardassians have a vulnerability there, just as humans do.
As for Odo's vulnerability, as I recall the writers explicitly stated that they didn't want Odo to come across as a superhuman, invulnerable fighting machine (as liquid-metal terminator had been). They wanted him to seem just as vulnerable as any other character, but with a few extra abilities.
If we insist on an in-universe explanation, it isn't hard to imagine a reason why Odo can be knocked out (or damaged by a Klingon weapon, for that matter). For example, humans are much more vulnerable to a knock out blow when they don't see it coming. When you see the blow on its way, your reflexes aid you. When you don't, they can't. So we could imagine there is something similar in changelings, where adjusting to adapt to a blow requires a sort of reflex or semi-conscious reaction that surprise can negate.
The changelings are established as being vulnerable by nature: they have been persecuted and hunted for eons by the solids. Since the whole notion of shape-changing beings is a fantasy, I have no problem with providing the additional suspension of disbelief necessary to imagine they can potentially be harmed by conventional means, at least in certain situations.
To be scandalized by Odo being knocked out, we have to assume that the decentralized anatomy of the shapeshifter removes the "weakspot" of the head, but what if the opposite is true? What if the weakspot is everywhere
on a changeling taken by surprise? In other words, perhaps a changeling is hyper-vulnerable and sensitive by nature, and his ability to rapidly adapt to an attack or change form is his only defense. It would make sense, given the Founders' paranoia and fear of solids.
Also, what is wrong with thanking the good doctor? Would it have been better if Odo had gloated about his invulnerability and told Bashir to go suck it?