Read Arduino code generated by Simulink
Simulink just supplies code for all the things you could be up to, triggered by a serial command of yours. This is very slow and I think it's obvious, that you would want a fast and slim realization of everything possible, if you attempt to do HIL.

If there is a special part you think is only easy for you with blocks, just ask right away, but it is really easy to do everything you can wish for in a few simple lines.
Also this is better for you, because you really know, what's going on.

I could provide some detail code, since I'm doing HIL myself atm, but you would need to specify a bit, what you are up to.

To really answer your question: I don't know of any other visual programming tool for arduino and as stated above, my best knowledge is, that simulink uses pretty messy things. And loads them onto the board right away, right?