I think the bigger issue than the extra "0" line at the start and trailing newline character is the fact that the site if outputting EWKB and EWKT and not WKB and WKT. I find working with EWKB frustrating at best, so in this case I would simply get the results as EWKT since it is easier to break it down into a valid WKT string.
The following works with Python3:
>>> from urllib.request import urlopen
>>> import arcpy
>>>
>>> url = r"http://uldk.gugik.gov.pl/?request=GetParcelById&id=141201_1.0001.1867/2&result=geom_wkt"
>>> req = urlopen(url)
>>> EWKT = req.read().decode().split("\n")[1]
>>> EWKT
'SRID=2180;POLYGON((674979.39 482566.88,674977.47 482560.5,674957.17 482567.55,674951.8 482552,674919.75 482562.88,674917.55 482555.33,674917.07 482555.46,674914.48 482547.58,674907.97 482549.88,674902.7 482533.84,674882.59 482540.6,674897.8 482593.03,674936.98 482580.48,674979.39 482566.88))'
>>> SRID, WKT = EWKT.split(";")
>>> poly = arcpy.FromWKT(WKT, arcpy.SpatialReference(int(SRID.split("=")[1])))
>>> poly.area
2379.763699999483
>>>