Is it legal to have a roomate who is on disability income and him to pay 5 percent of the rent?

of course, but if it is SSI, his benefit  will be reduced by 1/3rd if he is not paying his fair share.  there are a couple ways to determine what that is....either half the expenses if there are 2 of your (or maybe 40% if he has the smaller room)....or you can try 30% of his income toward rent/utilities.

realize if you charge him 400 for rent/utilities, you are free to pay some of his bills for him (other than food/housing).  for example, you could pay for his cell phone or transportation expense or maybe give him a walmart gift card for clothing.  he just needs to be paying a fair share of food and housing to get the full SSI.

SSDI is not affected by the rent arrangement.

Depends on who that 5% mandate came from. 

If this is low income housing then no you cannot live there unless you are on the voucher. An unauthorised tenant in low income housing is benefits fraud & a federal crime. If that 5% is an informal agreement between the 2 of you then there is nothing wrong with that as long as you are both approved & on the lease.  There is no law on how roommates split the rent.

Nothing illegal about that at all, why would it be?