That makes no sense given the age of some of tunnels in this region...
Yeah...that's completely false. The North River tunnels need a major rehab, which has never been done at a substantial level because taking one tunnel out-of-commission for 1-2 years reduces the NEC to single-track between Penn Station and New Jersey. This is a midlife overhaul that can't be put off or else major structural problems are going to come up making it unsafe to run trains. Nothing is being closed forever. Not here, and not the B&P tunnels...when that replacement is built the old decrepit one is going to be taken offline and fully refurbished so there's 4 good-condition tunnel tracks out of Baltimore.
That's the doomsday warning to build the Gateway Tunnel within 20 years...or else Amtrak has to do the painful thing and take 1 tunnel North River tunnel offline, rehab, then take the other tunnel offline. Which probably means delay-filled Amtrak-only traffic for years on end and all NJ Transit marooned at Hoboken Terminal for the full duration of the rehab.
The East River tunnels are already been taken offline one at a time for major rehab. Although that's not going to be nearly as painful because there are 4 bores instead of 2 and it's very slightly under-capacity. So that one won't cause delays for Amtrak or LIRR.
A lot of this is just flood protection. Both the North River and East River got fucked up by saltwater intrusion from Sandy. Track/electrical/signals were fixed immediately but the walls weren't and now the outermost concrete's starting to flake away and needs a full sealing. All of them have to be equipped with better drainage and flood barriers because this is only going to get worse with sea level rise.
At least the Portal Bridge is finally funded for replacement with a brand new high fixed span. That's the most decrepit piece of infrastructure on the entire NEC, the #1 most frequent failure point when the movable span gets stuck, and the #1 traffic bottleneck of them all because of the frequent openings and painful speed restrictions. New bridge is supposed to handle 90 MPH.
Norwalk River swing bridge on the New Haven Line is also finally funded for total replacement. That's far and away the most unsafe and delay-prone one one in CT. And it has to open way often because of commercial barge traffic. Being replaced by a lift bridge with separate lifts for each pair of tracks for redundancy. Lifts are way faster and less maintenance-intensive than swings, and can be adjustable height (which means only has to rise partway for barges).
Connecticut River Bridge is in expedited design/EIS...that's the last one needing replacement on the Shoreline, and the #1 Shoreline bottleneck. Still needs funding for construction, but that replacement will be a much higher bascule tall enough to rarely need to open.
Still impossibly deep in the funding hole for the other 3 New Haven Line movables, Susquehanna River Bridge in Maryland, and Pelham Bay in New York. The 3 CT bridges are likewise supposed to be replaced by faster/more reliable lifts, and Pelham and Susquehanna by high fixed spans (Susquehanna expanded to 4 tracks if they can afford it). That'll remove every movable from D.C. to Greenwich, CT except for Dock lift in NJ, which opens like once every 5 years and is in considerably better condition than the other legacy ones 'only' having been built in 1935 (it's just a baby!).