These wind lifted shingles are a common issue with these very popular 3 tab shingles. Check if you have any shingles laying around your property.
Leaves and tree debris can cause bigger leaks than you think. This particular one caused water to "poor" into the garage during a flash flood, backing up the water underneath shingles and under wall siding.
When a skylight is this bad, just replace it. They do not cost as much as you think to replace these domes and sealant.
Most of the time the common hail damage cannot be seen from the ground. Its best to get a good inspector out to inspect for any necessary repairs before calling into your insurance company.
Trees should not only be trimmed away from the roof to prevent the tearing of shingles, but they also should be trimmed at the thickest part to prevent a good wind gust from tipping it over or breaking off large branches to cause this type of roof damage.
These pipe jacks have a rubber boot that will only last 10 - 12 years (not as long as your shingle), and should be inspected and completely replaced as necessary. When they leak around the boot or even are lifted by the wind, they cause severe damage to the decking and obviously to the interior of your home.