Amtrak's current schedule is far less than that. They're running one regional every two hours. Several trips I had booked had SO many concurrent cancellations that I have 4 changed itineraries in the app followed by just "this service has been cancelled" in bold red letters instead of the normal qr code, and no replacement. To get a refund I have to call them...the app still charges a cancel fee. As an aside: dumb.
Thus, Amtrak can, and probably IS, absolutely clos(ing) a tunnel right now. They already did that on the weekends during off peak times. 6 trains an hour is more than demand warrants. Amtrak likely needs 2 per hour, that's it. They are not running hourly regionals, there are no Acela's, no Keystone's, no Pennsylvanian...Florida basically banned nyers from even coming in...other services are truncated. They can fit the LDs into the other slots for the hours they aren't running the Regionals. That leaves NJT with 4 slots, so two per hour each way. 1 necl, 1 njcl. Both should be sufficient for demand which is nearly 0. Essential workers can transfer at Newark or Secaucus or travel via Hoboken. If social distancing requires more capacity, increase train length rather than frequency. NO business traveler is going dc to nyc right now., nyc to bos, etc. For those who don't live on the nec: it is bad. If you don't have to go out, you're not going out. Face to face meetings may work better than teleconference but not so much better that it is worth the risk. So Amtrak can absolutely close a tube now and work on it. The question is will they get funding. Short term, no, they won't. They like everyone else in transportation are fighting for survival, and thankfully were just bailed out. They aren't going to start a major works project right now, but could do some serious emergency repairs if they can afford it. Medium term maybe. If this lasts another several months, congress *will* pass an infrastructure bill to try and restart the economy. You can bet your bottom dollar they'll include gateway in that. Not a sure bet, but it makes sense politically and it will be included after intensive lobbying. The impact to gdp by the northeast megalopolis is extreme, with the Hudson tunnels directly responsible for a large chunk. The horrendous impact this society altering event will have, means NYC will get stuff it needs, including these tunnels.
Also: I do not buy 6 per hour. That is an estimate if you use bidirectional flow. If you stack things so 30 minutes are northbound, 30 minutes southbound, capacity is more like 10-12 per hour if done right. And that's DEFINITELY more than enough.
I think at present, the tunnels are the least of Amtrak's, or NYC's worries. But, from a schedule standpoint, they could. I think some folks here overestimate how many people are currently using the tunnels and how many trains Amtrak or anyone is running through them. No one is traveling. The type of person who rides Amtrak dc to nyc is not traveling. The type of person who rides a long distance train is DEFINITELY not traveling. Think about the main demographic that rides Amtrak's sleeper cars. For coach, those folks have been furloughed. Exceptions exist but many airlines and Amtrak are reporting demand down by 90-99%. The only people using those tunnels are healthcare workers that work in NYC, and similar essential workers.