Of course, me being an electronics noob, there are some questions left:
1. As already mentioned above, can the CD40106 IC’s unused pins be left floating? If not, do I simply tie them to ground?
-> Good practice is to tie the unused inputs to ground; otherwise, the chips thend to use unnecessary power or even oscillate in some cases.
2. In that regard, aren’t unconnected AE Modular pin header sockets “floating” anyway? In Eurorack, 3.5mm sockets can be switching and may connect to ground when no jack is inserted.
-> In AE, digital inputs are pulled to ground by a 100k resistor; this is enough to tell the chip input "low" and high enough to not affect a "real" input signal.
3. I didn’t add any voltage smoothing capacitors, as I never quite understood when or how these are used. Are they necessary or recommended somewhere in my module’s circuit?
-> Generally it's a good idea to add a 100nF (approx.) capacitor near digital chips from +5V to ground; this has the effect to smooth the power supply from sudden minor changes caused by momentary higher consumption of ICs, microcontrollers. These changes might pollute the supply line and could then be audible.
4. All five elements (LFOs, Counter, OR Logic, VC Switches, WarpGen) are directly connected to the same 5V and ground. Do I need to add something to make sure that there is no crosstalk or harmful interference from one element to the other?
-> no worries; I see nothing here that could cause a problem. Synth circuits are usually very forgiving because parts are used far below any limits of operating frequency etc.
BTW: You made a nice thing - congrats!!