For what it is worth, some thoughts:
I own a 30 year "motorsailer" (Nauticat 43) with a 30 year old engine. I understand your argument, but I don't think it is so cut and dried. The purchase price will reflect the condition of the boat as a whole (engine included). However for me, what I wanted was original, as my experience with "improvements" by previous owners is that they are usually rubbish and all has to be pulled out. If the engine is low hours and well maintained, why change it? Modern engines are certainly more economical, but usually all computer controlled and turbo charged and high revving, the characteristics of which may not suit a 30 year old heavier displacement motor sailer.
For instance in my boat, I have a Ford 2722 4.5 litre 4 cylinder normally aspirated engine: 1500 rpm gives me 7.5 knots. Many owners have changed them for Yanmars and the like but the newer engines are much lighter and ballast has to be added under the aft cabin floor to compensate. Also all the engine bearers, gearbox, prop and often shaft have to be changed. PBO did an interesting article about re-engining and what struck me was that the final bill was something like double the cost of the engine alone, and the owner did a fair amount of work himself. I have changed my view to having the engine rebuilt (this is quite common with these Fords) when required at about half of the cost of a new engine alone.
So, look for a decent engine with plenty of spares availability, get a condition report and make up your mind what you think the whole package is worth. IMHO spend your time looking carefully at the condition and life span of any teak decks: that is the real ticking time bomb..
P