Ultimately we'll never know. There doesn't ever seem to be a concrete answer. So we can only speculate between budget, lack of resources ( @Saint Rubenio looking into it, there's def more that goes into PC dev because of all the variables, since PCs aren't uniform like consoles are) or, a third explanation i've seen: artistic value.
See, I've seen it suggested looking into this that because the art is the soul of Vanillaware's projects, putting it on PC where it becomes easily moddable is something they do not want. Take from that what you will.
I would say this is also probably why they never do sequels. A remake or remaster later down the line sure. But a sequel would require commitment to the IP (well not always but you get where I'm going with this) and sequels usually have to justify their existence with how well the previous title did. With Vanillaware making one and done projects, don't gotta worry about that.