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

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.

Do you think that 12AX7 Mullard long plates from 1950s would last longer than 12AX7 RCA black plates from early 1950s ? I would guess yes but I might be wrong.

They would not sound the same but that's another point.

"vintage 12AX7 and 12AU7 can last for 10000 hours if you are lucky” - it’s pure engineering, nominal usage conditions vs. spec etc.. harder driven devices last less..