I’m in the same boat.
Found this relevant issue: Plots don't show automatically when PyPlot compiled with PackageCompiler · Issue #476 · JuliaPy/PyPlot.jl · GitHub
You can get the figure to show in the notebook with display(gcf()) (or just end the cell with fig if that’s your figure object).
To actually restore the auto-display behaviour when using PackageCompiler, see this unmerged PR by @xzackli: add a flag which delays the init until IJulia cell by xzackli · Pull Request #480 · JuliaPy/PyPlot.jl · GitHub
It is installable with Pkg.add(url="https://github.com/xzackli/PyPlot.jl")