My *current* interpretation (and what I see in Snapshot 18w08b) is that gaps such as with pane glass or gaps between pane glass and glowstone will *NOT* be affected, water will *NOT* leak. From what I've read, fences and stairs would only have water flowing around them if placed within a water source block. Otherwise, they would block the flow of water as expected. I would suspect this will hold for glass panes. HOWEVER...
"Spit in one hand and hope in the other, see what fills faster."
If you can't test a COPY of your world in a snapshot (such as with an SMP server you don't control) then I would agree with @FuelZ's suggestion: board the windows up from the outside before the server upgrade, then test and see. I'd rather have my home look ugly unnecessarily, if covering them are NOT needed, than have my home ruined by not covering the windows. Good luck, but if I see different than what I've mentioned in this post I will most certainly post again about it here.
Oh yeah, check out DocM77's report on 18w08a with Ilmango and others in the Technical Minecraft Community (TMC). For anyone that thinks the new water physics might be a problem for their builds, the TMC watches for these kinds of things and how it may affect their Over Powered farms and such. If there are any changes to water physics that will touch their OP farms, the TMC is likely the first to find out and they will spell out exactly what is going on. Keep an eye on them. Something might slip past the TMC, but I don't think it likely.