I ran I to the exact same issue when following BlenderGuru's beginners' tutorial. I was confused and reloaded an old save. It turns out Andrew unhides his vertices at one point and forgets to show it. Try Alt + H before applying the modifiers and it should work
If you've already applied the modifiers go to sculpting and press'Grab' (yellow one) and press shift while clicking the holes until they are all gone.
If that doesn't work then select the vertices with the hexagon holes and then click f (to create a face there) however this is really inefficient and makes your donut look bad