What is the effect of equipment position?

There are basic technologies that can function alone and upgrades to those, which require the corresponding basic unit on your ship to do anything. These upgrades then can be further divided to those that don't depend on proximity to the basic module and those that have an increased yield when placed adjacent to the basic module.

Apart from this, there is no effect of the equipments' position, but I would advise building your ship in a way that makes inventory management easier (equipments and empty/filled cargo blocks separated as possible). This might require tearing down a module and rebuilding it at another place, but this can be tricky if the equipment has exotic ingredients. You would have an easier time if you did this strip-down and rebuild when in vicinity of an abandonded ship that provides you additional cargo space for juggling the resources. Also, be sure to plan ahead, to avoid situations where you dismantle something only to find that you can't rebuild it with the available resources.

Here is a list of the known (almost certainly all) modules, noting which upgrades benefit from having the basic module adjacent: Out There wikia