This does not seem to be a problem inherent to the ploltyjs library (Which is called by both Plotly.jl and PlotlyJS.jl by relying on PlotlyBase.jl).
I tried to reproduce the same scientific notation using PlotlyBase.jl and looking at the metadata of the plot object in the cell HTML (using the browser developer console):
So it does indeed seem to come out of some processing that happens between the call to plot and the translation to the plotly HTML code.