Yes, but they are probably surface mounted, meaning not a job for the faint hearted. It's do-able if you have the rework soldering tools & skills required for such a task. Better still is to mount PLCC type Sockets & then push new CIA's in.
I had this same problem with my A4000D. The mouse worked fine but the Joystick wouldn't track vertically. I had the CIAs replaced by suggestion and the problem didn't clear up. So I had the ports replaced. Didn't work. Then the Motherboard died. I don't want to scare you but that is what happened to me. Like others are saying though, replace the CIA's first and see if that fixes the issue. I wish you the best of luck!
I've got personal experience with both AmigaFrance and Anthony in NZ.
AmigaFrance I bought some Agni from. Okay service, but some people have been complaining lately.
Anthony is frist class. No hassle and no negative reviews. What ever is wrong with your motherboard, he will find it out. And if it's CIAs, I'm sure he will socket them for you and replace them. Atleast I know he has to working CIAs as I left a dead A4000k mobo with him for parts.
I cannot stress enough the quality of his work, and how competent and reliable he is.