Not always. A properly designed system can intermix the code quite easily, and Apple has already had the problem of intermixing code with Altivec, so 32/64-bit code is nothing special.
Depending on how the system is crafted, converting the 32-bit libs to be compatible with the new back end is simply grunt work. Co-existing is the least of the worries, as you just said that the routines that normally take 32-bit parameters would need to be updated to handle 64-bit parameters. Since this by itself breaks the usual specification, or there is a specification already available for quite a few libs MacOS X uses for 64/32-bit compatibility, this is also simply grunt work.
And here is the rub, the work required to do this is actually smaller than you think. While it is work, and it does need to be done, it is grunt work. It will not warrant splitting the OS into 32-bit and 64-bit versions that people keep claiming. Show me proof that it is a significant complication to the system to support 32-bit and 64-bit calls within the system (more than the current complication of detecting and adjusting to Altivec at runtime), and I can believe you, otherwise I find it hard to believe that this fairly minor arch change would require such a large split in development.