My understanding here is that the masorah here is relating to the word שְׁפֹט / שְׁפוֹט without any prefixes.
That word does appear only twice in Tanach: here (spelled defective) and plene in II Chronicles 20:9
אִם־תָּב֨וֹא עָלֵ֜ינוּ רָעָ֗ה חֶרֶב֮ שְׁפוֹט֮ וְדֶ֣בֶר וְרָעָב֒ נַֽעַמְדָ֞ה לִפְנֵ֨י הַבַּ֤יִת הַזֶּה֙ וּלְפָנֶ֔יךָ כִּ֥י שִׁמְךָ֖ בַּבַּ֣יִת הַזֶּ֑ה וְנִזְעַ֥ק אֵלֶ֛יךָ מִצָּרָתֵ֖נוּ וְתִשְׁמַ֥ע וְתוֹשִֽׁיעַ׃
where, interestingly, it would seem to be a straightforward noun (equivalent to the word מִשְׁפָּט).
(There also seem to be other versions of the masorah which quote a third instance: the word שְׁפָט appearing in Proverbs 31:9.)