Indeed a share without an engine fund is worth less than a share with an engine but that is buyers choice not a valuation of the aicraft itself. The straight value of a share is the value of the aicraft divided by the number of shares. No engine fund I would be knocking money off the value of the share but would not add value to the share just because a fund existed. Putting a new engine in does not magically restore the devaluation of an airframe that arises from an extra thousand or two hours being put on it!
Lets buy a diamond DA40 new. £100k (easy maths) spllit it 4 ways, £25k each. Fly it for 2000hrs. Put a new engine in, is it still worth £100k? No it has devalued in addittion to the engine wear. But a new engine in using the engine fund is the share still worth £25k? I would say by that point you are looking at a 5 year old aicraft and would say the share is only worth £20k now.