Whether your house was built a hundred years ago or yesterday, no one builds a roof the way they build a floor. Roofs are designed to hold up under wind rain and snow, that put steady pressure all over the roof's surface at once. Because it's a practical way to build them, they're also designed to hold up the guys doing the work. But unlike your floor, no one much cares if that sort of tromping around flexes the surface, or booms like a drum. Shingles are inherently flexy. It's scary, but safe enough (if they're harnessed) and will be over soon.
There may well be a bit of flex/vibration that transmits from the roof through the timbers to the walls and ceiling, and it might be enough to open a crack or two, especially in an old house with real plaster not drywall. The round holes you noticed in the wall are likely caused by that flex popping the skim coat of plaster off the screws holding drywall to the structure. It's only an aesthetic worry, unless there's a whole lot of plaster damage, or it's showing a pattern that follows the structure behind it, and indicates a weakness in it. A tube of Polyfilla™ from the hardware store should fix it. But it's always worth a conversation with the roofers, who should be aiming for no damage, and who should have an eye for underlying structural issues (especially ones that let them off the hook), and you might just find you've lucked into the A-class team that'll fix it.