.htaccess issue

I just want to know that if i add some web optimization rules(eg: gzip, exp headers, etc) on .htaccess file, will it cover all the sites inside the network?

Yes, if you place them above the WordPress .htaccess section. For example, hotlink protection, setting expiry (ala W3TC), etc. does it that way.

My root site got 100/100 and the sub-site got 93/100.

He… he… got a 100/100… *thunk* ??

See if the Yslow reports what it thinks is a little off. It may be that the subsite is using a plugin that isn’t optimal. The root site may not be using that plugin.

There was one CDN related issue, after fixing that it’s 99/100 now.
The only difference is in “Expires headers” section. There is 1 static component without a far-future expiration date which is https://subdomain.mydomain.com/favicon.ico. I’ve added exp rule for ico type but don’t know why it’s not working for my subsite.

I’ve run into that too, sometimes Google Speed and ySlow just ignore the .htaccess setup, and I’ve never figured out why.

I’d take the 99 and have a beer, personally.

??