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We have huge problems with fingerprint files - taking up 50 gigabytes of disk space on a machine which is already stressed for storage, taking a long time to copy anywhere, taking Jenkins itself a long time to compact the fingerprints...
Storing them in one file certainly seems to be a good fix. I'd almost suggest using a relational database for it, since a lot of time seems to be spent figuring out the links from a project which used the file to the project which generated the file.
Our build generates at least 100 artifacts, so presumably the workaround for us would be to zip some of them together into a larger file which would be uncompressed at the next build.
Quick statistics from our build server: