...i believe this is the nature of placed .ai and also .pdf files that have only one ink, eps on the other hand doesn't produce this behavior...
...something to to do with the pdf format that illy uses to create 9, 10, CS or CS2 .ai files that you can place into indesign...
...saving to a legacy format lower than 9 is one way to get around this, however you may encounter problems doing this as formats above 8 have features that won't hold in formats lower. Transparency being the main one, so best to keep it in the format it was created in wherever possible...
...it can be handy to have these extra plates in some cases as a way of previewing that artwork hasn't inadvertently been put onto unnecessary plates. I always output to all seps in a seps workflow, so as to check through on RIP preview before committing to proof or final output...
Andrew