Yes HTTPS is used. The thread doesn't say that the web app will be completely insecure, instead it says
This effectively reduces the security of your end-to-end encrypted communication to that of your SSL connection to the server
Which means that anyone who can control the SSL connection to the server can now intercept and break your e2ee communications. So who exactly can control the SSL connection?
Well, if a (state-level) attacker controls/compromises a CA, they could issue a fraudulent certificate for the Signal server and attempt to MitM the SSL connection (this threat is limited by the use of certificate transparency.) As @multithr3at3d pointed out, TLS inspection proxies at workplaces are a much more likely form of MiTM and could cause problems if your employer was interested in compromising your private conversation. However, in such a case, the employer owns the machine and would probably just install a keylogger on it, so you have bigger problems.
However, the larger threat here is that the SSL connection, as well as the content being served, is controlled by the Signal server. This means that if the server is compromised or goes rogue (which can easily be achieved by a government serving Signal a subpoena or the like), then it can easily modify the js files served to the client in a way that allows them to intercept the communications. This effectively defeats the point of end-to-end encryption, which is that nobody other than the sender and the recipient should be able to read the contents of the communication, since the server now has the power to compromise the communications at will.
This threat is amplified by the fact that such malicious modification of the code served can be done in a targeted manner. The server can ensure that only a specific user/client is served the modified malicious code. This significantly reduces the chances of the modifications being detected and exposed.
Actually we want to develop some chat service like signal with web-client, but this article made us confuse about should we ship a web-client or not, can anybody please explain it?
This depends on your threat-model (or rather the threat-model of those who will be using your chat service). Will those people just be using it for chatting with friends or communicating with colleagues? Or will it be used by whistle blowers trying to coordinate the disclosure of classified information with journalists? You will have to consider whether the risk outweighs the benefits and decide for yourself whether or not to ship a web client.
If its the former, then having a web client will not be a very big issue. This is closer to the use-case of WhatsApp and WhatsApp does have a web client.
If its the latter, then you had best follow Signal and stick to using desktop clients and apps which can be signed and their integrity verified.
As evident from the comments some people are confused about why these issues don't apply to the app and desktop client.
The reason is simple. The app/desktop client has to be downloaded once. It is also digitally signed so its integrity can easily be verified. If you are paranoid, you can also download Signal's publicly available source code and compile it yourself. If Signal attempts to publish a malicious update, they will have to publish its source code as well, and the chances are much higher that someone will notice the unexplained changes before any damage happens.
With a web app things aren't so simple. First of all, even if the web pages are digitally signed, checking their integrity and ensuring they match the publicly available source code every time is absolutely impractical. Secondly, a web app consists of several web pages. Checking the integrity of all of these even once would be a painstakingly difficult task.