I believe I may have found a solution I like for the Cypher Conundrum. In a nutshell, what I call the Cypher Conundrum is a convergence of two things in Numenera and The Strange.
First, if a GM generates cyphers randomly on-the-fly, he's going to end up with some results that don't make sense. Some might say, "That's ok, Numenera's supposed to be weird, and The Strange is, well, strange," but I think that. There's a difference between something that doesn't fit and is weird and strange and something that doesn't fit and is just dumb or ill-conceived.
Second, players in the Cypher System are supposed to find (and use) cyphers all the time. If you run many of the published adventures, you'll usually find that PCs are finding cyphers faster than they can use them, for a variety of reasons. This often leads to cyphers being left behind, which can be a drag for the GM if he's creating and detailing cyphers ahead of time.
As a way to address the first aspect, I've started really thinking about context when I come up with cyphers. Where are these cyphers coming from? What materials are available?
I don't worry so much about what the cyphers do, as with hyper-advanced tech, who knows what's possible? But I do worry about materials. If the PCs are scavenging the remains of an Accelerator, for example, they're unlikely to find cyphers made of cloth. (An Accelerator is a mechanical, self-aware automaton).
In the case of the Accelerator, most materials would work--metals, crystal, glass, synth and ceramic are all materials one could conceivably find within an Accelerator. So in this instance, I just roll on the table. If I get a result that doesn't work, I either reroll, or perhaps just change the material.
If the source of the cyphers is more limiting, then I look through the tables for ones that will fit. For example, a recent encounter involved a biological organism that yielded cyphers. I looked for any cyphers that made sense, and I also took some cloth cyphers and made them leather (hide) instead. Easy peasy.
There are other times you'll want to do this as well. For instance, in Numenera adventure, The Hidden Price, the PCs find a cache of cyphers that are all made of glass and crystal. It's relatively easy to find cyphers that fit the bill and take others and just change their material to glass or crystal. Not only does this make more sense and not break suspension of disbelief, but you're also in effect creating new cyphers (or at least new forms of cyphers) that are unique.
I almost always come up with cyphers ahead of time (which I highly recommend). Now that I'm putting more thought into where they come from, it makes it a more active process than just rolling randomly, and I find I more often have an idea of a cypher or oddity to throw in that's of my own creation, or of a slight variation on one that already exists that especially fits.
The other part of the Cypher Conundrum, you'll remember, is that so many cyphers you come up with are "wasted". Either the PCs never find them, they throw them away, they explode in a mishap, or something else happens that results in your lovingly-created cypher never seeing any action. However, it's so easy to reskin things in this game, that I just keep those cyphers in a master list and use them again sometime down the road--either with another group, or a long enough time later and with enough cosmetic changes that the PCs won't recognize the recycled cypher as something they've seen before.
I do believe the Cypher Conundrum exists, though some choose to ignore it, and others don't care about it that much, and that's fine. However, I've found that working through, for myself, how to solve the Conundrum has deepened my game and my world. Even if my players never notice (I think they will), it doesn't really matter because it makes my Ninth World more concrete and real to ME, which in turn allows me to present it much more convincingly to my players.
Lately I've started handling cyphers a little differently in my Numenera games. Instead of making specific cyphers for specific places or encounters, I instead make a master cypher list for each campaign I run. I fill the list with a bunch of cyphers, and I just come up with what it is, what it does, and the level. Then, when PCs find cyphers, I choose ones from my list and come up with what form they take at that time. I check the cypher off of my hard copy of the list when I give it out, and then I delete it from the digital copy once they use it. That way, if they discard a cypher, I can give the same cypher out again at some later date (or even in a different campaign) with a different level and form that it takes.