Will 12AX7 tubes in phono and line amp last longer than 12AU7 driver tubes ?

I would say keeping at least one 12AX7 and three 12AU7. 

When the 12AU7 in the driver circuit fail on one channel, I would say it is better to replace the 12AU7 for both channels.

Johnny

IIRC, 12AX7's have a higher output than 12AU7's, so that's a consideration, as well.

Talking vintage high quality tubes. The amp is VAC Avatar SE integrated.

How many spare sets should I have ?

i don’t have personal experience with your vac model, but in my travels with other vac gear, i would say kevin tends to run the tubes fairly hard in terms of biasing etc, so i would keep 3 good sets around ... 

"12AX7's have a higher output than 12AU7’s” ax7 tube has higher gain than au7, but lower nom/max cathode current, thus shorter lifespan at similar bias/loading etc. 

I only have one spare set for 12AX7, 12AU7 and EL34.

I understand, good vintage 12AX7 and 12AU7 can last for 10000 hours if you are lucky, and some last even longer. I hope at least for 5000 hours.