Let me first say that your husband has the right to benefits.
Housing Benefit does not affect you, provided that you do not fall in one of the following categories
1. That you are not or both claiming it, although he can add you as member of household
2. That he is not claiming it because of you. If you have 1 kid together, the maximum you should get from council is 2 bedroom flat, if you get 3 bed flat, it will affect your applicatiion
3. That you are working. If you don't work, the case worker might conclude that he is claiming it because of you.
4. that you will not claim more benefits shortly after your Ilr is granted especially if you don't work.
My wife was getting housing and child benefit. I applied for ILR recently, declared everything and it was granted.
Regards