Seeing the sad numbers in the weekly chart, just over 2,000 worldwide, has me wondering when this site will stop tracking the Vita on the main page, like how the Wii U was abandoned even though it was "technically" still being sold. Physical carts are being halted outside of Japan early next year, so is that time? Will it be when there's a successor, assuming there is one? I'm curious.

They tracked the PS3 and 360 as late as last year. We will probably see it until 2020. Maybe even later.

I didn't realize that, but weren't those selling better?

Check for yourself 
http://www.vgchartz.com/weekly/42932/Global/

The Vita is selling better than both of them in that link. 360 is below 1k.

So, the time to stop tracking when the baseline falls to 1-2k?

I think it is when the system gets completely discontinued. 

I'd say same as the 3DS, well for different reasons obviously. The Vita is not selling anymore and the 3DS is going to be replaced full time by the Switch or at least I suspect that much. I don't see much future in the 3DS because of the Switch I mean.

So will we have soon a chart that has neither 3DS nor Vita? Maybe, in the meantime it does not hurt to have them both there right?

38k vs 3k is a huge margin.

Probably when media create stops tracking it.

If a console hasn't be discontinued, there's no reason to stop tracking, and if it hasn't been replaced there's no reason to remove it from the front page either.