Yes; the Payment of Wages Act,1936 stands applicable to shops and establishments beyond certain minimal strength of the no. of employees employed therein by means of notification by the State Governments and as such shops and establishments having 100 or more employees would be covered by the Industrial Establishments(Standing Orders)Act,1946. The second sentence of the post is a little bit ambiguous with incompleteness. I think what the questioner actually wants to know is whether the Act would continue to be applicable in case the no of employees falls below 100 at any point of time in a year. Once the establishment comes under the purview of the Act, the subsequent reduction in employee strength is irrelevant for its continued application.