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Whenever a journal asks for "Articles should be limited to 3500 words + 5 figures/tables", do they mean the texts in the tables and figures will not be counted in the 3500 words limit?
Also, will the reference section be included in this word limit? Or, it just means only the Abstract, key-words, introduction, methods, results, and discussion sections will be bound to 3500 words limit?
That depends on the journal. Therefore you should ask them.
E.g. https://aip.scitation.org/mmm/authors/jsprep (mirror):
Contributed MMM Manuscripts should not exceed 3500 words. Abstract, title, author list, references, and acknowledgments are all excluded from the 3500-word limit. Figures, tables, and equations, however, are included and must be accounted for by calculating a word count equivalent to the space they occupy.
https://jasn.asnjournals.org/sites/default/files/ASN/PDF/jasn_ifa.pdf (mirror):
Original Articles are limited to 3500 words (including significance statement, abstract, and main text, excluding Methods) and eight data figures. Methods, references, figure legends, and tables are not included in the word count
FYI Why do so many publishing venues limit the length of paper submissions?
