Cat hides all day because of medication

If stopping medication is not an option then you need to create some opportunities in the day that do not involve medication. She needs to see you as more than just the delivery vehicle for tastes she doesn't like. If she takes off after getting medication, is there a toy or laser light you could have ready to entice her back with?

What about catnip in the area? Can you block access to her favorite hiding spot so she is forced to stay out in the open? Can you vary the times you give her the medication?

For us, we don't want one of the animals to be scared and always nervous when one of us approaches. We've had a kitty that reacted much the same as yours is and it broke my heart when she ran from me whenever she saw me, even if I was just coming to pet her. Her meds were stressing us all out. She hated them, hated me and I didn't think it was right that her final days were spent in fear so we stopped the medication. Mind you, we tried every which way to Sunday to get her to take them. She simply didn't want them. So we stopped. Did her sub-q fluids at the vets office instead of me doing them at home. Stopped forcing food and meds. She came back to my lap, didn't run from me as much and became her old self. It was a tough decision, but she was happier. And in the end, she spent her final time here enjoying us and her home. That is after all, the most I could have hoped for. Painful as all get out for us but she was at peace.

Good luck with whatever you decide to do.

Have you voiced your concerns to the vet-this is alot of stress for one and 2nd maybe there are options of other meds/different schedule.

Also see if the medicine can be compounded with a flavor she likes-ask the vet/pharmacy for more info.
I personally have a cat with a 4-5 heart murmur(no treatments are being given)

You can even alleviate the concerns of the pill with Greenies pill pockets. You mentioned that you didn't think it would work, but they aren't that expensive to just try out a small bag of the chicken flavor ones.

Otherwise, you can dab the pill in butter and that way at least its delicious and slides easy.

The best advice I can give you, which has saved my relationship with my cat, is to get a cat bag.
I made a video a while back of me pilling Bugsy with it - here you go: Why I Love my Cat Bag
Bugsy went from completely avoiding me at all times, hiding under the bed, to not caring at all - it removed the stress from our relationship. It has been nothing but a life-saver. I have used it with all my cats succefully - I rely on it completely.
The most user-friendly is Called Klaw Kontrol. It is awesome. The most durable one is called the cat Sack - this is the one I am using one the video with Bugsy.... For someone who is beginning to use bags, I would definitely recommend the Klaw Kontrol - IMHO it is hard to beat that bag.... Once you are used to it you can "upgrade" if you want. I use the cat sack because Bugsy is a BIG cat (18lbs).
For pills, I do not use Pill pockets- they don't work long term (at least for any of my cats)- I use Purina Whisker Lickin's treats - the soft ones... I smash one on the palm of my hand, put the pill in it, and form the treat over it again. Works like a charm every time - Have been pilling Gracie for 8 months this way, 2x a day, never failed once.
Hope this helps!