To get "propper behaviour" the distribution just have to pick three data directories (ie. /usr/share/kde3, /usr/share/kde4, and /usr/share) and determine where each program should reside (eg is it KDE3 only, KDE4 only, or a regular application) and set the default XDG_DATA_DIRS values appropriately (eg "/usr/share/kde3:/usr/share" in KDE3 and "/usr/share/kde4:/usr/share" in KDE4).
If using only one data directory, you will get duplicates of every entry in the K-menu that is available in both versions, and if using only two directories you will get the "two separate worlds" you describe, but both those scenarios are due to bad distribution packaging, not due to anything KDE did wrong.
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