Are switched jacks ever used for in-system-programming connections? (If not, why not?)
There are several issues with switched connectors in an ISP app:

Too few pins!

Switched connectors are only available in configurations with a few (2, 3, maybe 4) contacts -- many in-circuit programming interfaces need more connections than that.

Too big!

Switched connectors are usually of the audio-jack style, and many of the more exotic configurations require a chunkier connector body, typically only seen in 6.35mm, which makes the connector quite large and costly, compared to more typical ISP connectors.

Too bouncy!

Like any other switch, the switches in a switched connector contact bounce -- this could throw off the circuit if a "live" connection or disconnection was made.  While the connector contacts experience contact bounce as well -- the programmer can work around this by tristating its side of the connection, allowing hotplugging of the programming connector safely, something that'd go away in your proposal.