it is a possibility it could be seen that way yes but that's generally unlikely but before you got a bit too much "into" nofollowing links etc. wanted to make you aware of it.
With the tag what you're sort of saying is"these pages are all very similar this is the first one and this is the last one" Google's pretty cleaver and most people don't give it credit if your site is about real estate etc. it will know your listings may be seen else where for example in the UK we have Rightmove & Zoopla they both list properties from else where but they also have value in other aspects of there sites which is why they work, so as long as your site is not just about the pages that are duplicates and you give worthy content on other areas generally you should be fine. Make the site really helpful for the user and the rest sort of falls into place you can also take the time to look at how they've solved the same problem.
Regards to the 3000 pages, if you can get some unique content on there fantastic but i know its not always easy. Your original question was about the risk of nofollow, there is no risk with it, now its really your choice with the noindex tag. I can imagine you can leave it on but you may risk not being all you can be, I would suggest taking a look at your competitors and other similar sites to get an idea of what they do in a similar situation.
you might find this answer helpful which is on the same subject - http://moz.com/community/q/real-estate-mls-listings-does-google-consider-duplicate-content