It seems that when you specify yref='paper' in a subplots in add_shape this is ignored (I saw this by doing print(fig) on the fig object). You can force the behaviour by doing
from plotly.subplots import make_subplots
import plotly.graph_objects as go
import numpy as np
rng = np.random.RandomState(10)
a = rng.normal(size=10)
fig = make_subplots(1, 2)
fig.add_trace(
go.Histogram(x=a, histnorm='percent'), 1, 1
)
fig.add_trace(
go.Histogram(x=a, histnorm='percent'), 1, 2
)
fig.add_shape(
go.layout.Shape(type='line', xref='x', yref='paper',
x0=0., y0=0, x1=0., y1=0.9, line={'dash': 'dash'}), row=1, col=1
)
fig.layout.shapes[0]['yref']='paper'
fig.show()