Not saying it can't happen but would be more inclined to believe mix in gene pool than everything being blamed on bee pollen variations.
That depends completely on the particular daylily.
Some diploid daylilies are self-compatible. That means they will produce seeds from their own pollen. Other diploid daylilies are not self-compatible. Some daylilies have flowers that are often visited by insects while others have flowers that are seldom visited by insects. Some daylilies have flowers in which the anthers are relatively close to the stigma while others have anthers which are further away from the stigma. Some diploid daylilies have flowers that produce pods without any hybridizer having hand-pollinated them.
That means the hybridizer must be wary of what they think is the parentage of the seedlings they produce depending on the characteristics of the parents and they methods they used in making their crosses.
What I have found out is that even after staying within strain for over 3 decades recessives genetics still crop up
That can certainly happen if the appropriate crosses have not been made in the previous generations. However, one cannot get the "dominant" characteristic appearing when crosses are made between two parents showing genetically the same recessive characteristic. One can however get the "dominant" characteristic appearing in some of the offspring when crosses are made between two parents that although they appear to be showing the same recessive characteristic are actually only showing the same phenotypic characteristic and it is genetically different in each parent.
