After being in Airplane mode I configured the Airgap Vault on the phone and received the 24 words seed phrase along with the recovery key and I also created my cryptocoins addresses. Now my questions is , since I ve done all of this completely offline how will the blockchain know about my address and private key? I don't understand how something that was created on an airgapped device completely out of the world can be a part of the blockchain which only exists online, I think . Now I am afraid to send the money to that address because I don't know if it should've been done while I was still online or the way I did it was the right way to do it.
Blockchain doesn't have to know your address or anything. Addresses are not stored in the Blockchain and is just a derivation of your ECDSA public key, together with some additional information. You absolutely do not have to be online for this. Addresses are never "registered" with any central authority or stuff. In fact, when you're generating an address, you're just generating an ECDSA key pair on the secp256k1 curve which has a random 256bit number which is incredibly big. The probability of another individual generating the exact same key is astronomically low.
I want to mention that for security I reset the phone to factory and connected it to a safe network(as it can be these days) to be sure there is no malware. But still, the only way to have the app installed was to connect it to a network therefore it was not airgapped, reset and never went online . This way I think malwared could have come either from the network , or from the app itself I suppose... Would be a better idea to transfer the files through bluetooth , sd card or anything else ?
I don't know about the app that you're using. I would never use a phone as an airgapped set up. Unless you sideload the application using APK or something similar with prior validation, there is a good chance that you've accidentally downloaded a malicious version of the intended app. I'm not sure what's the probability of this happening but I've seen plenty of those fake apps on Google Play recently.
2.About the airgap pc , I've read that when you send the transaction to the airgap pc you can also have the malware that's why would be better to use unwritable usb or cd's and destroy after every use. But if the malware is there it can send information through various ways: Electromagnetic,Acoustic,Thermal,Optical. What can it be done to be secured 100% against these methods in the case you take the malware .
Hardware wallets are specifically designed to reduce such signatures and if you're paranoid about that, you have to use a hardware wallet. There is no way around it.
As to whether the malware can copy information from the offline computer, I'm not aware of any viruses that are as advance as this. I'll say that there is a fairly low chance as such malware would be fairly complex to be able to achieve such a feat by exploiting the vulnerabilities within the signing app and having it to execute a malicious code as well. I don't consider that as a huge risk.
3.My concern is that trough these methods they can take maybe more easily the private key from a phone. Or maybe not because you don't have to send the transaction physically therefore there is no possibility for malware infestation unless it was there before first setup. Am I right? In this case 2 phones using qr codes would make it safer than an airgapped pc?
You can use QR codes as a transfer medium using airgapped PCs as well. IMO, given the relatively small number of mobile users as compared to desktop wallet, I wouldn't see their level of security to one that would rival Electrum, Bitcoin Core and other desktop wallets.
4.My last question is , if I use the phone as an Airgapped device should I try to destroy bluetooth/wifi/antennas hardware (if there is any way) or is it safe to leave it as it is? I don't know if there is a way for the hacker to disable my airplane mode and making my phone go online to steal my private key.
If you're paranoid, then you should.
If you're inexperienced with cold storage set up, I would strongly dissuade you from pursuing such implementations. They are fairly confusing and complex for the average newbies and could result in unnecessary problems and headaches. In the case of Ledger, for which other than the database blunder, has been performing fairly well, it's a good HW wallet. If you're scared about the wallets being tampered, you should be scared about the bootloader/firmware of your phones being tampered as well. I wouldn't be surprised if there's some sort of intentionally inserted backdoor, though Apple has publicly refused but who knows? If you want a more open wallet, try using ColdCard.
I cannot recommend you to use phones as cold storage unless you know what you're doing. There is no way a phone could achieve the level of security that a hardware wallet can provide. If you have the money to spend and want to avoid headaches, go for hardware wallet.
If you still want to do this, consider using Electrum's method instead. It's quite a proven and tested method.
https://electrum.readthedocs.io/en/latest/coldstorage.html