A topic that definitely deserves more attention. Bravo!
The only major suppliers of silicone shell earphones are Sensaphonics (US) and ACS (UK). I'm not experienced with 1964 so can't comment on those except to say their site seems to be all about acrylic shells, except for sleeves made for universals. I probably missed a key link...
I've experienced both, and silicone is superior in every meaningful way. Keynote's summary is pretty good.
Comfort? No contest. Would you rather sleep on a brick or a pillow? Even if the brick has smooth, rounded corners, I'll take the pillow every time.
Isolation? Again, no contest. According to Dr. Brian Fligor, ScD (Children's Hospital Boston, Harvard Medical School), the expected difference in broadband isolation between acrylic shells and silicone earpieces is about 12 dB -- a significant advantage for silicone, and one that is especially pertinent to proper IEM design. YMMV.
Slight digression: From my perspective, the whole idea of "tuning" IEMs to the "acoustical environment" is kind of ridiculous. The entire idea behind BA IEM design is to approximate direct injection, essentially taking acoustics out of the equation. The driver is connected to a tube, which is inserted into the ear canal. The entire "room" that is being filled with sound (the space between the end of the earphone and the eardrum) is about one cubic centimeter (1cc).
Hollow acrylic shells are (relatively) easy to manufacture but IMHO mechanically weak. First, the drivers are physically mounted to the shell, opening up the possibility of unwanted vibration. Second, they are much more susceptible to harm, as hard shells can crack when, say, stepped on. Third, they are hard, which means they are (a) less comfortable (ever seen hard plastic earplugs or hearing aids?) and (b) that the seal can be broken, compromising bass response.
In terms of manufacturing, silicone is indeed much more problematic to work with; nothing sticks to it! Acrylic shells can be basically machine-made, requiring a human only for component assembly and polishing. Medical-grade silicone doesn't lend itself to automated processing, so every step is done by hand. Sensaphonics has a team of experienced artisans armed with Dremel tools to craft all earphones in their in-house lab. This increased labor cost is significant, making Sensaphonics are real bargain compared with the manufacturing cost of acrylic shells. (ACS uses a similar process afaik, but obviously I don't speak for them.)