It is hard to determine the exact cause of the difference in performance without more information on the system, or an example model. From this simple information, you are replacing a simple system with a more complex one and it takes longer; that behavior is not unexpected by itself. Furthermore, these equations scale with i, so one would expect any difference to be exacerbated as i increases in value.
However, it is important to understand that Simscape systems are handled differently than regular Simulink systems. In Simscape, the "==" operator is used to represent continuous mathematical equality, which is not synonymous with assignment, i.e. the equations are not solved sequentially. In other words, using multiple equations would not simplify your system; it would just replace a single equation with a system of equations.
You can find more information on how Simscape language solves equations in the documentation: https://www.mathworks.com/help/physmod/simscape/lang/defining-component-equations.html#brn4h9l-3