As someone who has had the engine, shaft and stern tube out and finished getting it back in a mere hour before the booked craneing in, (*NOT* reccomended, I tied up the lifting berth over the fortunately non-working weekend hooking up the fuel, exhaust and electrics), change *any* thru-hulls you aren't 100% confident of.
The exhaust one should be above the waterline so its not going to sink you but the cooling intake and any galley or heads ones and any thru-hull tranceducers must be in A1 condition with good sealant and backing blocks glassed in place.
Make sure that all seacocks and your stern gland are perfect and then you can launch with confidence and with a little talc around the possible problem areas to show up any weeps early, you'll be able to check them before you have to pay for extra time in slings.
Replacing anything iffy that you cant shut off with a known good seacock is a lot cheaper than paying for extra crane time or lifting out again.
Change out the Exhaust through hull, you *dont* want the extra back pressure from a restriction. If you are reinstalling the same engine, change the exhaust hose from the engine to the waterlock if you've had any overheating due to blocked water intake etc. Inspect the waterlock carefully and replace if its been overheated (the inlet barb can collapse under the jubilee clip) or there is any cracking from frost damage.
Replace the cooling intake hose, the liner on some types of hose can collapse under suction with nothing visible externally once the bond to the reinforcement weakens with age - pick up a little weed and you may not be able to restore cooling flow even after clearing the filter or you may get random overheats you cant track down. The rest of the cooling system after the pump is under pressure and if the hoses are sound and the anti-syphon loop vent tests OK can be reused .