If I decide to add say an Audigy and M-Audio Audiophile 2496 PCI card to a two year old tower (Athlon 64 3000) am I likely to encounter any issues or will the kernel do it's magic?
That is always tricky to predict, but there are some places you can look:
To see if the cards are supported, you can have a look here (make sure you read the comments about what does or does not work)http://alsa-project.org/main/index.php/Matrix:Vendor-Creative_Labshttp://alsa-project.org/main/index.php/Matrix:Vendor-MAudio
Another good place to look is in linuxquestions.org's "hardware compatibility list":http://www.linuxquestions.org/hcl/showcat.php/cat/81
(creative labs hardware)http://www.linuxquestions.org/hcl/showcat.php?cat=all&stype=1&si=m-audio
Is there any reason to use 2 soundcards? It'd probably be a lot easier to just use one, I don't know anything about using 2 soundcards simultaneously, but it's probably gonna be very tricky to set up just right.
That processor should be fast enough for making music.