It depends on what they're acquiring you for. If they're acquiring you as a team of great programmers and they see your code is shit that probably isn't good.

If they're acquiring you because you built a product that has great adoption in the marketplace (YouTube), but your code is spaghetti they won't care very much.

If it's based on revenue they really won't care.

In most cases your core team will be required to stay on at the new company long enough that any missing documentation will have had time to get written.