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See also Seattle’s SR99 tunnel and Boston’s Big Dig (though the latter is 15 years old now).

Tunneling through an existing city, often near water, is just hideously complex and expensive.

I remember when I was in Boston a discussion of how to expand one of the T-lines under Tufts Medical Center without causing vibrational problems for the equipment in the hospital right above.

That's a non-trivial engineering challenge.

Have the hospital cease usage of the equipment and relocate appointments for that equipment.

Gonna be awkward to shut down a major children's hospital in a city for an indeterminate period of time.

Who said you need to shut down usage of the whole hospital? Just usage of those specific machines.

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