1) My main concern is , I like online wallet like bitcoin.com, trustwallet etc.. where they provide private keys and 12 words secret phases. Can they have still have custody of my coins anyhow? Is coins stored on their server?
First of all, bitcoin.com is a known scam site designed to promote a bitcoin fork known as Bcash. You should avoid it. Secondly, as I said above Trust wallet is closed source, so you should avoid that too.
To answer your general question, any closed source wallet could have access to your private keys and coins. Since it is closed source, you have no way of knowing what it is doing. It could only give you pre-generated seed phrases from a list known to the developer, or it could send your seed phrase off to some server somewhere where someone else could access it (like Coinomi did when they sent seed phrases to Google servers).
You should stick to open source software wallets like Electrum, or go one step further and get a good hardware wallet.
2) In hardware wallet, does coins are stored in hardware? or only private is stored in a hardware wallet? Eg. suppose if there is 0.1 BTC in our wallet it is stored in address and can be seen in blockchain ledger so actually coins are stored in wallet address on blockchain server and not on hadware or software wallet. Am i right? or not?
You are right. As PawGo has explained, coins are not stored on your hardware wallet. The only thing which is stored on your hardware wallet is your private keys, and these give you permission to move certain outputs around the blockchain.
Thanks for your answer.