That's a very nice question based on Rashi's Pshat (1) in the Gemara.

We know that Rashi on Chumash (2) also cites this explanation, actually from the Tanchuma.

I see that the commentaries are also bothered by your excellent question.

The Ramban (3) rejects Rashi's interpretation in part because of your question. Instead, he explains based on the color of the Techeles.

The Mizrachi (4) cites those who try to answer by saying that the appearance of the prefix Lamed in the third occurrence of the word Tzitzis actually counts for three missing Yuds, since Lamed in Gematriya is 30.

The Mizrachi himself, however, rejects this explanation. Instead, he contends that this Derashah is following the opinion that "Yesh Em l'Mikra," which considers the pronunciation of a word to be its primary characteristic, rather than its spelling.

The Sifsei Chachamim (5) with this as well.

The Gur Aryeh (6) disagrees with the Mizrachi's contention, because -- he argues -- even if one holds that "Yesh Em l'Masores" (the spelling of a word is its primary characteristic, rather than its pronunciation), nevertheless here it is legitimate to base the Gematriya on the full spelling of the word, since that is the proper name by which people refer to this object, even if it is not spelled that way in the Torah.

I hope this helps! Best wishes,

Yishai Rasowsky