It's true that you should never give your birds anything at all in their drinking water, not vitamins, not any medications, etc., because #1) You have no idea how much you are giving your birds, and #2) It contaminates your bird's water immediately.
Your birds should not need any type of multi-vitamin supplement as long as they are eating a healthy diet that includes lots of fresh veggies, fruits, a healthy seed-mix that is low fat and contains no sunflower seeds or nuts, and hopefully a fortified pellet. And if you insist upon giving your birds a daily multi-vitamin supplement, it should be one that is either given to them directly by mouth once a day and suggested by your Avian Vet, or at the very least should be an Avian multi-vitamin that is in powder-form, and that you sprinkle on top of your bird's staple food (either pellets or seed-mix) once daily, and that comes with a pre-measured dosing scoop, such as Qwiko Avian Multi-Vitamin...But never put anything in your bird's drinking water...
Now as far as your question about "apple cider", I'm not sure what your ultimate goal is, as you mention not putting a "vitamin drop" in their water anymore, which is good, yes, please stop using cheap vitamin drops and putting them in your bird's water; However, "vitamin drops" have nothing to do with "protecting your bird against bacteria or fungal infections" at all. So you're actually talking about 2 different things; the only reason you would want to give your bird's a daily multi-vitamin would be to ensure that they are getting adequate amounts of vitamins and minerals every day, which again, they really don't need if you're feeding them a healthy, well-rounded diet. But regardless, a vitamin has nothing to do with boosting their immune systems or protecting them against bacteria or fungal infections...
I think what you're talking about isn't "apple cider", but rather "apple cider vinegar", which is used in certain circumstances in birds to protect against fungal infections, for example, if you are hand-feeding a baby bird hand-feeding formula and the baby is having issues with yeast in their crop, slow-crop, or crop-stasis, you can add a few drops of "apple cider vinegar" to the hand-feeding formula to help the issue resolve itself...As far as just giving your bird apple-cider-vinegar as a daily preventative supplement against a possible bacterial or fungal infection in their crop/GI Tract, I've not heard of this being done unless the bird is suffering from an active fungal infection, and then they do this buy adding a drop or two of apple-cider-vinegar to the bird's drinking water (don't ever give your bird straight apple-cider-vinegar, as it is very acidic)...
I'm sure there are people who do put apple-cider-vinegar in their bird's water every day, but in my opinion you'd be much better off by instead giving your bird a daily Avian Probiotic, which will keep your bird's natural levels of healthy, normal bacteria throughout his GI Tract up, thus naturally protecting him against any type of fungal/yeast infection developing. I give all of my birds a Probiotic on their seed-mix every morning for this purpose, and none of them have ever had any type of GI infections. Probiotics are simply giving your bird the exact same strains of healthy bacteria that they naturally have throughout their GI Tract, or should have (if they are taking an antibiotic for a bacterial infection, the antibiotics will kill-off even the healthy bacteria in their GI Tracts, thus opening them up to developing a secondary fungal/yeast infection)...I use Qwiko Avian Probiotics, which is a powdered Probiotic you sprinkle on top of their pellets or seed-mix once a day, and which comes with a pre-measured dosing scoop. You can buy them at any Petco.
As far as having success from adding apple-cider-vinegar to your bird's daily drinking water, hopefully someone else can attest to how effective it is, as I've only used it during hand-feeding babies and by adding it to their formula to treat slow-crop....