Hi Graeme,
There's no real disadvantage to running your system at a slightly lower sample rate. It simply lowers the audio bandwidth by a small margin. Still, 44.1 kHz is CD-quality. I don't think that small 10% reduction will be noticeable to anybody!
When you change your sample rate, be sure to follow this tutorial in order to make everything behave properly!!
FAQ: How do I change the samplerate of my SigmaStudio system?
Regarding your question about AES/EBU, Toslink SPDIF, and Coax SPDIF...
The ADAU144x only has one S/PDIF input pin, and it takes two channels of audio, un-encoded, which follows the S/PDIF consumer standard. It has no decoding functionality.
If you only need to get one input at a time into the DSP, you can use an external switch in your system to select the source in hardware. That's easy!
Remember, this won't work with encoded audio data! It will only work with raw PCM.
However, if you need to take multiple S/PDIF inputs simultaneously, then you'll need an external IC that can take S/PDIF input and generate an I2S output.
Additionally, remember that your S/PDIF source(s) are asynchronous to the ADAU1442. This means you will need to use ASRC(s) to re-synchronize the audio to the local ADAU1442 clock.