Yes, There will be raw water (fresh or salt, depnding on where you boat) sitting in there. At the very least, open the seacock and let the system drain, then drain the raw water strainer. However, I installed one of these on the inbound side of the A/C raw water strainer:
This allows me to drain the A/C system, then remove the bypass 'thingy', replace it with a hose connector, then connect a short garden hose to the system. I have a small 1/3 hp pump that I drop into a 5 ga. bucket of Marine/RV antifreeze (Propylene Glycol), and pump the AF through the system. It displaces any water in there. This is done with the seacock closed, so I leave it closed. This prevents me from needing to prime the A/C system in the spring. Though technically, with the bypass, that wouldn't really be a problem either. The same system allows me to dump barnacle buster and water in the bucket and essentially 'descale' the AC system in the spring.