Saltcod-still not exactly understanding what you are saying. Although I have no personal experience with a Canoe Cove 41, my CC53 was fitted with Capital transmissions, and separate Walter Vee-drives, behind Detroit 6-71s. I expect your installation is similar, as CC used this configuration on many, many boats. Neither my transmissions nor my vee-drives were fitted with internal oil coolers. Mine have external shell-and-tube water-to-oil heat exchangers on each trans and vee-drive. These are plumbed to the raw water side of the cooling system on each main engine.
Should survey reveal the presence of water in the transmission or vee-drive lubricating oil, this is definitely not healthy, and should be dealt with promptly. Typically, water in the oil means a leaky oil cooler. How much water, when, how long ago, how much damage has already been done, etc. are moot issues-there's simply no way to tell. Find the leak(s), and fix 'em. If you are still in the pre-purchase phase, make it a condition of sale. If you suspect the vee-drives or transmissions have suffered damage due to water in the oil, I'd run for the hills, as repair/replacement of either is REAL spendy. Ditto if some moron bypassed the coolers, as they do require cooling for proper long-term function. As I'm sure Walter will tell you.
Personally, If I was OK with function of the running gear, I would require a cost reduction on the purchase price commensurate with material and labor costs required to remove, pressure check, repair/replace, and re-install any cooler that was suspect. I would NOT ask the seller to fix, as who knows what he/she might do to "fix" the leaky cooler(s). Than, immediately after completion of sale, I'd change the lube oil in the running gear, continue to take periodic oil samples, and watch the condition like a hawk for some time to make myself happy that no permanent damage was done to the running gear.
Hope all turns out in your favor. Canoe Cove built wonderful boats, with first-class installations, and unless a previous owner has been terminally stupid with maintenance, should last a long, long time.
Regards,
Pete