I voted yes.. But on a dual pickup guitar, i always replace the tone knob with another volume, so the pickups would each have seperate volumes.. Especially if I'm playing in the middle switch position..
I never use tone controll i feel like it muddies up the tone. i want each string to be heard and with the tone knob turned it just sounds bassy and yeh. having 3 knobs aligned like that does make for a pretty picture but thats about it
If you chooses the correct passive pickup your guitar will sound how you want it to sound without a tone pot. I rarely use tone controls with passives, and tend to think they degrade the sound.
However I think tone pots are essential for dialing in the exact sound you want from an active pickup, especially if you are trying to dial in a specific clean sound. I don't feel there is nearly as much sound degredation when using tone pots for actives.
So I would say yes they should continue to make guitars with tone controls. Most people like them, you don't have to use them and they can be bypassed if you want to optimize your signal path.
that said, If I were ording a custom shop guitar It would most likely only have a volume pot.