The copyright owner could sue for infringement, and possibly collect money damages. In the US, statutory damages can be as high as $30,000, or up to $150,000 for "wilful" infringement, or as low as $750 (per work infringed). Or actual damages can be collected instead. In other countries, actual damages plus costs of suit are more likely, but the rule can be different in each country.
The possible exceptions to copyright vary significantly in different countries. In the US the major exception is Fair use. See Is this copyright infringement? Is it fair use? What if I don't make any money off it? and I have a question about copyright. What should I read before I ask it? for more information In general short snippets of code can probably be used under fair use, but substantial parts of the code or the displayed site are less likely to qualify as fair use.
And if it is illegal then why are there so many legal open source or paid software and applications for cloning of website like httrack, cyotek, webcopy etc?
Most of these tools have legitimate uses, including learning how a site is constructed without distributing copied content; and cloning or partial cloning of a site with permission. Even if the tools were mostly used for unlawful copying, that might well not be a high priority for law enforcement, and cross-border law enforcement (which this in many cases would involve) is often much harder for the police and other authorities.