The Vanguard is a long thin hull, with a large flat missile deck. Even a small amount of trapped air will seriously upset trim, as the long hull will provide a greater distance for an air bubble to run up and down. The flat deck makes it easier for air to get trapped, and with a small scale of 1/100th, vents tend to be a bit on the small side.
You could make a couple of the missile hatches hinged, so that any trapped air in the casing pushes them open as the boat submerges. With a couple of those open, you effectively have a huge vent in your hull. Small weights glued underside the hatches would help gravity make them self close once the air was expelled.
If you look at subs from say WWII, the decks were full of slots and holes to enable the casing to vent quickly for rapid dive times, which could mean the difference between life and death for the crew.
With modern nukes, dive times are much more relaxed, slots and holes are a source of drag and noise, so are minimized. For models this can present a problem sometimes, as we don't want to wait minutes for our models to submerge, no matter how authentic it may be.