As both 1 & 2 are digital, the amp will be the decoder so really there should be no difference between the two.
Using option 3, I presume that you will have 3 matched pairs of cables for the 6 separate signals in a 5.1 setup? As you are conveying an analogue signal the quality is likely to be not as good as from options 1 & 2 however this does assume that the quality of decoder in the DVD player is the same or not as good as in the amp.
For DVD surround I use an optical cable from DVD player to amp. The amp does the digital to analog decoding. This offeres me the best surround sound for DVD.
For SACD, and CD audio, I find that the same DVD player offers a slightly better sound quality when it does the decoding. A bit deeper bass and more mid range clarity. So I use a pair of high quality phono cables and let the DVD player do the decoding, passing trhe analogue signal to the amplifier.
I would suggest that you set up 6 phono cables from the DVD to amp as well as an optical or co-axial digital cable and switch between the two to see which you prefer. If you cant hear a difference then stick to the 1 digital cable for convenience.