That's a lot of questions

Been thinking about it, I'll try to answer at least some of them.
First - battery. Trying to run the whole thing off of batteries is unrealistic unless you have a really big battery. You really ought to plan on using a "wall wart" to power it. If there is something you need it to remember through power interruption (calibration constants?) you can run the microcontroller in an interruptible sleep mode for a long time off a coin cell. Or simply have your code write the things you need it to remember into EEPROM whenever they change.
As an aside, several of my own clock designs use the coin cell method to keep time (in the controller, a 328P) through power outages, The designs pre-date things like ESP-8266 that now make NTP sync over WiFi easy, and if the Dallas RTC-on-chip existed then I didn't know about it. Anyhow, the 2032 coin cell keeps the 328P powered well enough to sleep and wake up once per second to increment the time. Potentially the battery lasts a very long time (never really tested it to extremes).
Driving the tubes. You can learn a lot on this subject by studying the schematic and analysing the code of one of Ian's open source clocks, You can make the high voltage using Ian's technique of using the 328P to control a basic boost circuit, Or you can get a MAX-1771 based HV power module cheap from a number of sources. I;d recommend using a 1771 based module but YMMV.
Most of the other tube driving stuff is already worked out for you - just look at Ian's open source clock schematic and code to see how to drive 6 tubes then scale that down to 4 tubes. That will get you on track for making a multiplexed display scale using one 74141, four optos, etc, If you want direct (non-multiplexed) drive, forget the 74141 and optos, and use two Microchip (nee Supertex) 5530s instead. 5530s are my method of choice but again YMMV.
I'd use an Atmega328P-PU as the controller, but that's mainly because I know it pretty well. It's a well established chip (it's the heart of Arduino UNO these days) and it's stable in my experience.
I just realized that I'm assuming you are planning to design your own board for this project. If I'm wrong, and you really want a kit (as the topic of the thread actually says!) then most of the above does not apply,,, oops. As far as shields and other ready to run stuff, I don't know very much. I'm not aware of a shield that runs 4 tubes but that doesn't mean one does not exist. "Shield" implies "Arduino". Except for the backup battery stuff, which may not even be necessary, I guess you could do it with an Arduino and some sort of shield. That's not a subject I'm well versed in - I do this stuff for fun, not for business, and I enjoy the challenges of designing from scratch and getting boards made rather than using Arduinos and shields.