My theory is that Shinji could have partial Dutch ancestry.

1) In both the Shinji Ikari Raising Project he’s wearing a bright orange shirt in the profile page for the video game, and in Vol. 8, Stage 51 of the manga he’s wearing a soccer jersey labeled with “NETHERLAND” and “14”.

2) His blue t-shirt under his school uniform is very close to the same shade of blue on the Dutch flag

3) Orange is the national colour of the Netherlands, being used on the Prinsenvlag, which has a similar shade to Shinji’s casual t-shirt in the NGE: SIRP game

4) The blue on his plugsuit, depending on how it’s rendered could be seen and sharing same shade of blue to flags of South Africa under apartheid, New York City, Albany, the Bronx, Jersey City, the Royal Dutch Navy, and Hofstra University

5) In a scene of Evangelion 3.0 + 1.0: Thrice Upon a Time explaining Gendo’s backstory, a clip is shown of UBE Industries’ chemical plant in Ube, Japan with a baby crying in the background, just before it cuts Yui Ayanami holding a newborn Shinji in her arms soon after giving birth. This implies that Shinji or his father were from Ube, Yamaguchi Profecture. The city of Ube is not far from Nagasaki, which is where the former Dutch trading outpost of Dejima is located. Dejima under the Tokugawa was restricted to Japanese and Dutch of certain professions. It could be that one of Shinji’s ancestors was Dutch who married with a Japanese, with their child being forced to stay in Japan.

6) The orange in the outfits mentioned with Shinji could be seen as a contrast to the red worn by Asuka in both her plugsuit and personal wardrobe in the NGE: SIRP manga, which is one of the national colours of Germany, which is the country of Asuka’s heritage

I don't think that's the intention. Most of the colors there are just common colors to have a shirt in, and SIRP is glorified fanfiction that got a publishing contract, with no involvement of the original writing staff, and should not be taken as evident of anything in the main show.

I'm dutch myself, and other than noticing that the "rood-wit-blauw" (red white blue, this combination isn't even unique to the Netherlands or its colonies) of the flag matching the plug-suit colors... hmmmeh, a bit too farfetched, especially if you need extracanocical media to support your theory.