As the others have mentioned, it will not cause problems to have duplicates and there are many times when the duplicates are desired. I created the combined ".dll" at ZKL before ZA created combined ".dll" files of their own. But it makes sense that if a building/fence is downloaded from here that there be a combined ".dll" file from here containing the building/fence id. Also, in order to not use up the ids faster than necessary, we often use the same id and same message for more than one building/fence/sold item, when it is appropriate. These can often be at different sites, each with their own combined ".dll".
As for removing individual ".dll" files, there are 2 reasons. First, many of the early ".dll" files were made from a modified version of the ingame lang0.dll. That can definitely cause sporadic game crashes for those with expansion packs. So those should not be used. They are easy to spot since they are larger than 1.8 mb in size. The other reason is just so Zoo Tycooners do not hit the ".dll" limit in ZT.