They will. This was a major design risk (read: design mistake) I made in deferring the consequences of your actions over the next installments instead of wrapping it up at the end of Hallowford, but the decisions you may could certainly come back to haunt you, and the connections you make in Hallowford may or may not prove a persistent thorn in your side or a major help further down the line.
I do, and your thoughts seem to dove-tail with my post-mortem (as well as the post-mortems of a few others) quite well. The fact that Hallowford didn’t offer much in the way of concrete character advancement beyond personal relationships and the possibility of grabbing the Heart was in retrospect, a major decision error, and I’m keeping that in mind in future.
One thing you may be overlooking is the fact that the reason the bodies have to be so well-preserved is because people come and visit them. That not only includes descendants and surviving associates, but also people wanting to take a look at great kings/queens/heroes etc as a tourist attraction or as inspiration/due to the mystical powers their bodies might be rumoured to hold. The best parallel would probably the practise of pilgrimage in Medieval Europe, where thousands of people travel over long distances to visit the relics of saints entombed in certain cities (like Canterbury) which benefited massively from this trade.
In short, the Cryptkeepers aren’t so much kept afloat on payments for crypt space, but by the stream of visitors who spend money in Hallowford’s inns and shops, which as you might have noticed, are also mostly owned by the Cryptkeepers.