If a quarterly journal wants to publish a special issue, should it be published as an additional issue or it should replace a regular seasonal issue? Are there any guidelines on this or it's a matter that depends on the journal's policies?
Both ways are possible, but usually they are called differently. If the issue is replacing a regular issue, it is called special issue.
If the issue is added to the standard set of issues, making an extra one, it is usually called supplement. And even here the conventions differ; some supplements are published with a regular issue, and some are published separately. Most often, they are numbered as
1A or alike, but form an integral part of the volume.
As far as I know, special issues replace regular issues. Sometimes a special issue may have a part dedicated to regular papers.
To make an example, this webpage lists the special issues of the journal Metrologia (a monthly journal): you can see that those issues follow the regular numbering.