I wondered whether thought experiments actually can be substituted for actual experimentation. I understand that in some cases it might be necessary, but can it be unnecessary over thinking sometimes? Which can cause controversial understanding of that subject.
Physics is the construction of mathematical models that describe the real world. For example, when Einstein formulated General Relativity it was just a mathematical model. Not until Eddington (debatably) observed the light bending predicted by the theory did it become accepted as describing the real world.
So research can be split (although it's a slightly artificial separation) into two parts: the theoretical construction of the models and the experimental testing of the models. Thought experiments are an essential part of model construction. They can assist with the formulation of models and test for internal consistency. For example, Einstein claimed that it was his thought experiment of an observer in a freely falling lift that guided him towards the construction of GR.
There are areas of physics where experiment has fallen far behind the theoreticians, notoriously in the area of quantum gravity. Whether this renders further thought experiment unnecessary is debatable. My own view is that while we can afford to build cruise missiles we can afford to provide theoreticians with pencils and paper (and wastebaskets, unless they're working in (insert your least favourite area here) in which case the wastebaskets aren't needed :-).