Hi @Chri, welcome to the forum 
That depends quite a bit on the size, surface, and shape of the thing. In the extreme, a very small object will have negligible effect, while a cup over the back of the thruster would prevent it from doing any useful work at all. Everything else will be on a scale in between.
I’d suggest having a read of this comment to help develop an intuition of how thrusters operate, and how that affects their flow near other thrusters and fixed objects.
How accurate does the calculation need to be? It’s very likely that an intuitive understanding would be sufficient for guiding your design, by thinking generally in terms of pressure differentials and flow lines. If you need to quantify it then you can set up a fluid dynamics simulation, where there are varying levels of complexity you can include (do you only care about one thruster + the manipulator? do you need to simulate the full vehicle dynamics? do you need to consider material surface properties, or water properties? etc).