There were plenty of extended closures for WCRM. All lines for a week in August(s), at least twice, somewhere south of Rugby.
It won’t be 125, partly because of the air pressure issue, and partly because Kilsby has very difficult geology (seams of running sand) and keeping the track fit for 125mph would be a significant challenge.
It’s not so long ago that midweek daytime trains had extra time in the schedules for a slow line weave to allow for maintenance on the fasts. Unthinkable now.
Re the other tunnels, the Pendolinos are pressure sealed, so can operate at the higher speeds without passenger comfort issues. The pressure relief shafts were there to limit the impact of a Pendolino passing other types of train in the tunnels, most notably curtain sided swap bodies (eg the Tesco train) where the vehicles could have been damaged. Specific tunnels:
Linslade is sufficiently short that it didn’t need pressure relief shafts (and the down fast is single bore so wouldn’t need them anyway)
Northchurch: the early feasibility used some old maps, only later was it realised that a new housing estate had been built on the land above the tunnel. The top of the shaft can be seen clearly on google maps.
Stowe Hill: already had plenty of ventilation shafts, but not quite good enough aerodynamically; IIRC additional audits were mined between the tunnel side walls and the existing shafts.