Written by Dyami Millarson
Considering that Germanic cultures and languages are thoroughly Indo-European, the Vanir are exceedingly unlikely to be non-Indo-European religious substrate. Almost nothing survived in Old Germanic languages and cultures from pre-Indo-European times; as we can see from the fact that the Ancient Germanic language and culture was thoroughly Indo-European as proven by the descendant languages and cultures, the Indo-European heritage prevailed and this must also have been the case with religion; the situation we observe in Old Germanic languages and cultures must be reflective of the religious situation as well: predominantly Indo-European. The battle between the Vanir and Æsir should, therefore, rather be explained in an Indo-European context.
I have seen people theorising that the Vanir are the Gods of Western European Hunter-Gatherers or an Indigenous European population. As of 19 March 2023, the Wikipedia page on early Germanic culture characterises early Germanic culture as “[l]argely derived from a synthesis of Proto-Indo-European and indigenous Northern European elements” without providing a source or explanation which we can argue for or against but later in the article the topic of a symthesis is brought up again when the following is said of the Vanir: “Germanic religion appears to have emerged as a synthesis of the religion of the Indo-European speakers who arrived with the Corded Ware culture and the indigenous populations among whom they settled. It is often suggested that the conflict between the Æsir and Vanir, the two groups in the Norse branch of the Germanic pantheon, represents a remembrance of this synthesis.” That is extremely unlikely to be true, when we consider there are, for the rest, practically no traces of them in the Ancient Germanic language, culture, and religion. Furthermore, we can connect Vanir to an Indo-European root and therefore we can explain it as Indo-European; there is no need to make this overly complicated, and assume some remnant from Pre-Indo-European times. The simplest explanation is just that the Vanir are of Indo-European origin.
Regarding Proto-Germanic vocabulary, I am aware of the Germanic substrate hypothesis, which aims to explain some words which have no cignates in other Indogermanic languages, and I have encountered discussion of it in etymological works, particularly those of the Dutch tradition. It is, however, a hypothesis, not a theory. Furthermore, I find the amount of words that can possibly be fitted into this category to be practically negligible when we consider Proto-Germanic consists of a whole sea of ostensibly Indogermanic words. One may look for non-Germanic words in that sea, but one should not make a mountain out of a molehill, or as we say in Dutch: one should not make an elehant out of a mosquito (men moet niet een olifant van een mug maken). For quick reference, one may take a look on Wiktionary at the small number of Proto-Germanic words that could be construed as pre-Indogermanic, and one may take a look at the currently approximately seven times larger number of Proto-Germanic words that is of uncertain origin, bearing in mind that having no satisfying explanation for Proto-Germanic lexical items does mean by default that they are of non-Indogermanic origin.