TVS Diode Array with EMI Filters on ADC Input

The TVSs on the inputs makes sense and your layout looks reasonable. The question is how far do you want to go to get what level of protection? It's a probability game. Just the TVSs should take care of most ESD events.

If you want to go a little farther, put a resistor in series with each input before the TVS, not between the TVS and the CPLD. This gives the TVS some minimum guaranteed impedance to work against. Going even farther, add a little capacitance accross the TVS. That will slow down the edges of really fast spikes so that the TVS can catch them effectively. It goes on and on, with each level of higher complexity decreasing the probability a damaging event will be encountered even further.

Only you know what environment these boards will be in, the cost of the extra board space, and the cost of failure.

It's usually a good idea to put an anti-alias filter in front of the ADC's input and if this also removes unwanted noise from the signal that is also useful. However, I don't think the filter is the full answer to why your circuit suffers "variations" when disconnected from the AC supply. You should try using a resistor potential divider to halve the dc rail to your ADC and feed this into the input to see if it is (somehow) and ADC problem or an external problem. It could be a problem with wires on the input and there ability to pick-up AC magnetically or it could be something else.

It's also worth saying that allowing a little high frequency noise thru with your signal can lead to high resolution results - it's called dithering.