There are two reasons for my warning; one of which still applies to the high voltage CMOS 4094.
Concerning 4094: You are thinking about problems that do not exist. Reading out a display is done by eyes and not by ESD-fingers ;-)
Would you use individual transistors?
For multiplexing you always need transitors for driving common anode or cathode pins.
Looking at ATmega48 the total current of VCC or GND is 200 mA. Divided by 8 segments (incl. D.P.) each segment can get about 25 mA which is delivered by a single output pin (max. 40 mA). But the common pins has to be able delivering 200 mA. These currents need a transistor anyway.
Multiplexing of 8 digits will reduce the eff. segment current to 25/8 = 3.1 mA done by current limiting resistors. That is enough for high efficiency LEDs.
Whether you like multiplexing or not depends (for me) of the hight of the digits. Displays <= 10 mm (0.4") are simple to root so multiplexing should be preferred. Displays >= 12.7 mm (0.5") offer a lot of space below them or on the other side of PCB. So it is very easy to use parallel driving (SMD 4094) and cascading many more digits as by multiplexing.
If you use larger digits >= 50 mm (2") where each segment consists of two or more LEDs you need transitors too. Here again parallel driving is the best way. Multiplexing would cause high peek currents and a lot of noise. ULN2803 is a compact form of segment drivers up to 24 VDC.