C (clang), 248 bytes

#include <ftw.h>
#include <fnmatch.h>
#include <regex.h>
*l,i,j;*k;regex_t r;f(n,s,t){if(fnmatch("*.sh",n,0))return 0;k=fopen(n,"r");for(regcomp(&r,"^\\s*(#|$)",1);i=getline(&l,&i,k)>0;)regexec(&r,l,0,0,0)&&j++;}main(){ftw(".",f,1);printf("%d",j);}

-5 bytes thanks to @ceilingcat

-14 bytes thanks to @cleblanc

Added the necessary headers and made it start in the current directory

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C (clang), 248 209 bytes

#import <regex.h>
*l,i,j;*k;regex_t r;f(n,s,t){if(fnmatch("*.sh",n,0))return 0;k=fopen(n,"r");for(regcomp(&r,"^\\s*(#|$)",1);i=getline(&l,&i,k)>0;)regexec(&r,l,0,0,0)&&j++;}main(){ftw(".",f,1);printf("%d",j);}

Try it online!

C (clang), 208 206 203 189 bytes

*l,i,j;*k;regex_t r;f(n,s,t){if(fnmatch("*.sh",n,0))return 0;k=fopen(n,"r");for(regcomp(&r,"^\\s*(#|$)",1);i=getline(&l,&i,k)>0;)regexec(&r,l,0,0,0)&&j++;}main(){ftw(D,f,1);printf("%d",j);}

-5 bytes thanks to @ceilingcat

-14 bytes thanks to @cleblanc

Try it online!

C (clang), 248 bytes

#include <ftw.h>
#include <fnmatch.h>
#include <regex.h>
*l,i,j;*k;regex_t r;f(n,s,t){if(fnmatch("*.sh",n,0))return 0;k=fopen(n,"r");for(regcomp(&r,"^\\s*(#|$)",1);i=getline(&l,&i,k)>0;)regexec(&r,l,0,0,0)&&j++;}main(){ftw(".",f,1);printf("%d",j);}

-5 bytes thanks to @ceilingcat

-14 bytes thanks to @cleblanc

Added the necessary headers and made it start in the current directory

Try it online!

C (clang), 208 206 203 bytes

char i,j,*l;regex_t r;f(n,s,t)char*n;{if(fnmatch("*.sh",n,0))return 0;FILE*k=fopen(n,"r");for(regcomp(&r,"^\\s*(#|$)",1);i=getline(&l,&i,k)>0;)regexec(&r,l,0,0,0)&&j++;}main(){ftw(D,f,1);printf("%d",j);}

-5 bytes thanks to @ceilingcat

Try it online!

C (clang), 208 206 203 189 bytes

*l,i,j;*k;regex_t r;f(n,s,t){if(fnmatch("*.sh",n,0))return 0;k=fopen(n,"r");for(regcomp(&r,"^\\s*(#|$)",1);i=getline(&l,&i,k)>0;)regexec(&r,l,0,0,0)&&j++;}main(){ftw(D,f,1);printf("%d",j);}

-5 bytes thanks to @ceilingcat

-14 bytes thanks to @cleblanc

Try it online!