Yes. The insurance price is calculated via ship and module prices, so every discount on that will reduce your insurance cost.
And it is actually worth it to replace your normal priced ship with the discounted one, even if you lose some money while selling the old one - worth it.
Indeed, the rebuy goes according to the value of your ship thus if bought with with a discount the value of your ship is lower than buying it without a discount. This applies to modules too.