If I only put the two entries from the question into a document with style=iso-authoryear I get
Dewachter et al., 2006; Diebold et al., 2006
in the citations. You say you get "Diebold; Aruoba (2006)" and that suggests that the uniquelist feature is involved (cf. Set limit to one author when using "et al." in biblatex). Presumably you have another entry where Diebold is also the first author, but that was not written by Diebold and Aruoba. (I faked such an entry for the example below.)
I personally find "Dewachter et al." for "Dewachter and Lyrio" unnecessary. Traditionally "et al." is seen as a plural abbreviation and should only replace two or more authors in a two-author list it may be slightly longer, but feels nicer, to also give the second author's name properly. I have no idea what your interpretation of ISO 690 has to say about that, but I could not find anything on this for citations in the English ISO 690. For the bibliography it only seems to be acceptable to use "et al." for lists of more than three authors (ISO 690:2010, 5.4.1 & 5.4.2).
I would also suggest to make diebmac06 a @report entry and not an @article. There might be a small problem with that at the moment (see https://github.com/michal-h21/biblatex-iso690/issues/70), but semantically @report is the much better type here. An @article should absolutely have a journal.
Finally, to your question.
If you want to see
Diebold a Aruoba (2006)
instead of
Diebold; Aruoba (2006)
you need to tweak finalnamedelim and multinamedelim.
The MWE produces the same results as an unmodified biblatex-iso in the bibliography, but uses comma and "and" in the citations.
\documentclass[czech]{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{babel}
\usepackage{csquotes}
\usepackage[style=iso-authoryear, backend=biber]{biblatex}
\DeclareDelimFormat{multinamedelim}{\addcomma\space}
\DeclareDelimFormat{finalnamedelim}{%
\ifnumgreater{\value{liststop}}{2}{\finalandcomma}{}%
\addspace\bibstring{and}\space}
\DeclareDelimFormat[bib]{multinamedelim}{\addsemicolon\space}
\DeclareDelimAlias*[bib]{finalnamedelim}{multinamedelim}
\usepackage{filecontents}
\begin{filecontents}{\jobname.bib}
@article{dewach06,
ISSN = {00222879, 15384616},
URL = {http://www.jstor.org/stable/3839071},
author = {Hans Dewachter and Marco Lyrio},
journal = {Journal of Money, Credit and Banking},
number = {1},
pages = {119--140},
publisher = {[Wiley, Ohio State University Press]},
title = {Macro Factors and the Term Structure of Interest Rates},
volume = {38},
year = {2006}
}
@report{diebmac06,
title = {The Macroeconomy and the Yield Curve: A Dynamic Latent Factor Approach},
year = {2006},
author = {Francis Diebold and Boragan Aruoba},
institution = {National Bureau of Economic Research, Inc},
type = {NBER Working Papers},
number = {10616},
url = {https://pdfs.semanticscholar.org/e876/92b94447574a05280cdf2e90ee1e77443a30.pdf}
}
@report{diebmac07,
title = {The Macroeconomy and the Yield Curve: A Dynamic Latent Factor Approach},
year = {2007},
author = {Francis Diebold and Aoragan Bruoba},
institution = {National Bureau of Economic Research, Inc},
type = {NBER Working Papers},
number = {10616},
url = {https://pdfs.semanticscholar.org/e876/92b94447574a05280cdf2e90ee1e77443a30.pdf}
}
\end{filecontents}
\addbibresource{\jobname.bib}
\begin{document}
\cite{dewach06,diebmac06,diebmac07}
\printbibliography
\end{document}
gives
Dewachter et al., 2006; Diebold a Aruoba, 2006; Diebold a Bruoba, 2007
in citations and
DIEBOLD, Francis; ARUOBA, Boragan, 2006. The Macroeconomy and the Yield Curve: A Dynamic Latent Factor Approach. Dostupné také z: https://pdfs.semanticscholar.org/e876/92b94447574a05280cdf2e90ee1e77443a30.pdf. NBER Working Papers. National Bureau of Economic Research, Inc.
in the bibliography.

If you have reason to believe that the default behaviour of biblatex-iso goes against ISO 690, against the Czech or Slovakian translation of the norm or even only against a common interpretation of the norm, please open an issue at https://github.com/michal-h21/biblatex-iso690/issues. Ideally you would include a full example document (not unlike the one in this answer) and could back up your claims about non-compliance with the norm with citations or exact references to certain clauses of the norm (or your interpretation of the norm).
uniquelist: https://tex.stackexchange.com/q/69028/35864. – moewe Apr 07 '19 at 15:22diebmac06is probably not an@articlebut rather a@report(or@techreport). It is also unusual to abbreviate two authors to "Dewachter et al." I would find "Dewachter and Lyrio" much more natural since usually "et al." is taken to be plural. – moewe Apr 07 '19 at 15:24biblatex-iso(which follows a stricter interpretation of the Czech version of the norm). ALL CAPS don't look very nice, the excessive use of semicolons and brackets for all kinds of information looks distracting ... The standard styles can be made far prettier with a few modifications. – moewe Apr 07 '19 at 15:26\thesis@require[backend=biber, style=\thesis@bibliography@style, sorting=\thesis@bibliography@sorting, autolang=other, sortlocale=auto, mincitenames=1, maxcitenames=2, uniquelist=false]{biblatex}– PK1998 Apr 07 '19 at 15:45thesis@bibliography@styleis defined as\def\thesis@bibliography@style{#1}– PK1998 Apr 07 '19 at 15:50