In Kri u-Khtiv, the vowels provided are for those of the Kri. The Kri of YHVH is usually Adonay. The first vowel of Adonay is Hataf-Patah. Why then is the first vowel of YHVH given as Shva in those cases instead of Hataf-Patah?
The niqqud we use today is that of the Tiberians. The default pronunciation of the shewa naʿ in the Tiberian tradition was identical to the pronunciation of the ḥataf pataḥ, and took on other qualities depending on its environment.
In some situations, such as under a gutteral letter, the vowel quality of a shewa would was less predictable; as such, ḥatef forms of vowels were used to remove ambiguity.
Before the stabilization of the ḥatefim in manuscripts, regular shewas were sometimes used under gutterals. For example, in MS Sassoon 1053 a "simple shewa rather than ḥaṭeph segol is used with aleph (as in אְלֹהִים)" (Yeivin, Introduction to the Tiberian Masorah, §34).
This image shows both shewas under gutterals and ḥatefim in MS Sassoon 1053:
Thus, Khan proposes that the ketiv form יְהוָה "is a vestige of a primitive stage of the development of Tiberian vocalization, in which a shewa rather than a ḥaṭeph sign was written on the ʾalef" (Encyclopedia of Hebrew Language and Linguistics, Ketiv and Qere).
i agree with @DoubleAA in the comments that it is just short-hand
but there can be another reason of the 2 versions
When, however, [the name] is written as י‑ה‑ו‑ה, there are those who pronounce the alef with a shva, for this is the vowel of [the corresponding initial letter which is] the yud of the name י‑ה‑ו‑ה. Others pronounce the alef with a chataf patach, using the same vowel as the alef of the name A-donai.