It's always good to have a fair idea of where you want to take a story, though this can be hard for one off projects. One of the things with shipping is if you hadn't planned on it and it comes up you might think Sure, Why Not?
This worked to great...well, to great effect
when fans really wanted Garrus and Tali
to be romance options, and BioWare
agreed. On the other hand, you might not like to take your characters in that direction for one reason or another, and if you as a writer doesn't support a particular ship then really you're the writer, you need to control how much of an impact fans have on what you write. If you don't want to support a fan ship there's no rule saying you have to.
As far as whether planning things in advance helps, sure. You could always give subtle hints in your story on where it could lead, then of course they could be subverted, Double Subverted
, however you think will work the best way.