is Lol skin (or any skin program) has virus?

yes and yes

You can use skin-programs on your own risk.

For now, custom models and artwork sit firmly in the “use-at-your-own-risk” category, but we’re keeping an eye on them. We can’t optimize for assets we don’t develop, and if they do become a concern for any reason in the future (ie. they provide measurable player advantage), we’ll take action based on the stance we just laid out.

Gray areas aside, there are definitely applications which are just not okay, and while the number of players in this space are very low (think a fraction of a percentage), we remain vigilant and hand out punishments to those who show patterns of consistent abuse.

We reserve the right to take action against applications that allow the use of our assets for free (often referred to as skin hacks).

Source: https://support-leagueoflegends.riotgames.com/hc/en-us/articles/225266848-Third-Party-Applications

You might not get a virus (wouldn't know, haven't used any mod programs) but they are bannable. It falls into a gray area, all 3rd party programs are considered to be "use-at-your-own-risk."