Fishing rod bobbers can go through Nether Portals, but disappear.
Sometimes they won't go through (especially if you are close to the portal) and will get stuck in the portal block itself.
The bobber will be reeled in when it goes through the portal costing 1 durability point. Yes, this can break the fishing rod.
Game output:
java.lang.NoSuchMethodException: zb.<init>(ajp)
at java.lang.Class.getConstructor0(Class.java:3074)
at java.lang.Class.getConstructor(Class.java:1817)
at sn.a(SourceFile:153)
at sl.c(SourceFile:2051)
at anb.a(SourceFile:71)
at sl.ac(SourceFile:851)
at sl.a(SourceFile:789)
at zb.A_(SourceFile:229)
at ajp.a(SourceFile:1589)
at lv.a(SourceFile:718)
at ajp.g(SourceFile:1567)
at ajp.k(SourceFile:1450)
at lv.k(SourceFile:551)
at net.minecraft.server.MinecraftServer.D(SourceFile:634)
at net.minecraft.server.MinecraftServer.C(SourceFile:562)
at ccd.C(SourceFile:154)
at net.minecraft.server.MinecraftServer.run(SourceFile:466)
at java.lang.Thread.run(Thread.java:745)
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Please update for latest 13w10a. Some times the fishing bob acts like it goes through the portal. Some times it acts like it bounces off. Sometimes it will get stuck "on" the portal. Also happens on Windows.

Already included in the description. Updated for latest current release and snapshot release.

Confirmed for 14w18b.

Is this still a concern in the current Minecraft version 1.8.1 Prerelease 3 / Launcher version 1.5.3 or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

Confirmed 1.8.1 pre3

Reopened, thanks.

Related to MC-96007
Can confirm for MC 1.12.1.