Does having content in Zotero folders cause duplication/performance issues

Just a quick query, since I'm new to the inner workings of Zotero. I have created some subfolders under "My Library" to organise my references. I notice that those references still appear under "My Library". I was wondering Zotero sees this as a duplication and whether this affects its performance. This is because I have about 3000+ references and Zotero has been incredibly slow. My file is roughly 150 pages and the size is 581kb. Any comments or suggestions will help. Thanks.

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