Application of the Payment of Wages Act, 1936
Yes, the Payment of Wages Act, 1936, applies to shops and establishments with a certain minimum number of employees, as determined by notifications issued by State Governments. Therefore, shops and establishments with 100 or more employees fall under the purview of the Industrial Establishments (Standing Orders) Act, 1946.
The second sentence of the post is somewhat ambiguous and incomplete. I believe the questioner is wondering whether the Act remains applicable if the number of employees falls below 100 at any point during the year. Once an establishment is covered by the Act, any subsequent decrease in employee count does not affect its continued application.