I agree she was rude @Cheeseandcoffee
A few posters have suggested the waitress was worried about you, in case you were drugged/being trafficked. Not impossible, but very unlikely. Most likely she is just a nosey, cheeky cow, who thinks she has the right to dish out her personal opinions to customers. And as you said, she would never have said this to a man.
I knew a woman (me and DH socialised with her and her DP for about half a year or so, around 2012, as her DP worked with my DH.) EVERY TIME we went out with them for a drink at the pub, (once a fortnight or so,) she said to me, with a tilted head and faux concern, 'are you OK?' I said 'yes' because I was OK. 'Are you sure?' she would say, 'because you look so tired and weary...' I was fine, I wasn't tired, and I didn't look any different to normal! 
I DID get tired eventually... tired of her fucking pecking my head and telling me I looked pale/unwell/tired/weary..... EVERY TIME WE WENT OUT WITH THEM. She would even say 'you're fidgeting a lot, are you in pain, are you stiff, are you OK?' (I wasn't fidgeting!) Then she'd say 'would you like to go out for a walk, and some fresh air.'
Eventually after about a dozen times of this shit occurring, I snapped and said 'I am FINE! Look, I tell ya what, if or when I am NOT OK, I will let you know. Unless I say otherwise, just assume I am OK!' She just took a sharp intake of breath, with a look that said 'ooooooooh.....' 
When I went to the loo, she asked DH what was wrong with me. '(He told me when we got home.) He told her I was tired of being told I looked tired and ill! She said 'well she she does. I can't help being concerned for her welfare.'
Suffice to say, we gave them both a wide berth from then on. Thankfully her DP left my DH's workplace a month after this.
Also, another thing that pisses me off is when someone says 'you look 'different!' That is NEVER a compliment. They are being fucking rude. I have also known other cases of people (checkout women, and bar staff etc) being rude. One woman on the till in Tesco looked at my friend's dark brown hair dye once, and said 'let yourself go grey. It's nothing to be ashamed of!' REALLY loudly so half the store heard her. Nosey opinionated cow!
And one barmaid commented on me having a third glass of wine once. 'Blimey, you're knocking the wine back tonight aren't you?' You've only been here an hour and a half, and you're on your third glass!'
For the record, I have 2 or 3 glasses of wine when I go to the pub, and then coke for the rest of the night, as that is my limit. But it was FUCK-ALL to do with her. It put me off going to that pub. Also, I only usually drink one or two days in every month, when we go to the pub.
Why people have to be so rude and opinionated just baffles me. They are either just ignorant and rude or probably quite stupid. (Or all of the above.) They are most certainly almost NEVER 'concerned' for you!