I will try to answer each issue separately as many are not related to each other.
Hydropnic clay pellets can be used to replace bark and still grow the plant like it was in bark. I have about 3000 in pellets with no water resorviour. they dry faster than bark but never need repotting as the clay does not deterioate like bark. When too large they can be lifted out and repotted larger without worry about cleaning the roots as the clay can remain clinging to the roots. the clay is also reusable. Since they can only reatan about 10% of the water on the surface, I can water late in the evening and not fear root rot.
the clay can retain slats and fertilizer buildups so they should be flushed every 3-4 months. (Just run water over them for a hour or so). Beacuse of the salt buildup I prefer watering from the top. Bottom water will build up salts in all mediums bark on orchids and dirt for tropical plants.
As to your Zygo I do not know where you live. Zygos do not like the Florida heat. It appears you are growing your indoors so the heat would not be the problem, but I find they like a lot of water. To flower they need more light then they will get indoors. I put their light needs just a little under cattleyas and the same as oncidiums about 2500 foot candles. 1/4 florida sun. I have not tried yet to grow zygos with a saucer of water, but it should work fine.
This Zygo bloomed for me January 2005, July 2005 and December 2005 before I sold it. so at least this species bloomed twice a year.
Dendrobiums lose leaves a lot. There are some that lose all their leaves each year, but even common dendrobiums will lose most of their leaves over a two year period. Usually they do not lose all at the same time but will when stressed. Typically they then grow new growths from the base, just like you discribe yours. You should get flowering on dens at least once a year on the new canes most in late spring early summer depending on lacation. If not then you need to give them more light. I grow mine in fiarly high light. some dens like nobile types want full sun all day long, so you can not generalise much. There are 180,000 different dendrobium hybrids and almost 30,000 different wild species.
I put half of 50 den seedlings (6 inch) in bark and half in clay last April and over the year all grew and bloomed and I did not notice any significient difference in the growth pattern based on the medium. I pot all in clay pellets now for convenience.