I am a bit confused just recently went through smart pls 3, How to choose between AMOS and Smart PLS, there are also many other software available for SEM. Does software affects the results ?
SEM (including AMOS) and PLS are two approaches that have some important differences. Indeed, some people would argue that "SEM" is not the best label to use when describing PLS.
Some of those differences are discussed here:
Article Reflections on Partial Least Squares Path Modeling
In a one line answer, Yes, indirectly software's does effect the results ( because it depends which software using which method to estimate the equations).
You can decide as per your research objective that which techniques you should opt.
Here are few few discussions, you may go through it.