No, PlusMaker's use of the smallest allocation block size does not affect your hard disk performance. All disk reads or writes, whether to files or the directory, are in disk sectors, not allocation blocks. The number of disk sectors read or written at a time is equal to the amount of data requested to be read or written unless the file or directory is fragmented. For example, if a 1 MB file is not fragmented, a request to read or write the entire file contents will be completed as a single read or write consisting of 2,048 disk sectors. The bottom line is that the file is made up of 2,048 disk sectors and that is all that matters.
Virtual memory is completely unaware of allocation blocks.
The virtual memory storage file is just a file. Just like all other files, all reads or writes to the virtual memory storage file are in disk sectors. It doesn't matter whether the page falls on an allocation block boundary or not. If allocation blocks are not 4K then it is possible that a fragmented virtual memory storage file will cause a page to be fragmented. With the new file manager in Mac OS 8.1 and Mac OS 8.5, fragmentation is decreased even with the smallest possible allocation block size.