You can “check the box” for a Half-Fare discount in Switzerland (CH) on bahn.de as well as on SBB.
I don’t know what process you are using to check prices, but I worked through the purchase process on both SBB and bahn.de and got very different results, depending on the date of travel.
For Wengen to Munchen on 12/06 3 days from now) on SBB:
With a Swiss HFC, 2d class, 109 CHF + 5 more for the reserved seat on the IC train Zurich to Munich
Without HFC, 132CHF + 5 for the reservation for a restricted ticket.
Full price flexible ticket w/o discounts, 161 CHF
For Wengen to Munich on 5/09, 3 months from now on SBB:
Super Sparpreis Europa, non-flexible ticket, 40 CHF with or without HFC
Flexible ticket with HFC 110 CHF
On Bahn.de for the same journey and dates:
For 12/06, €107 with the HFC; €131 w/o
For 05/09, Super Sparpreis of 39,90, no further discount for HFC
In summary: no difference in price between SBB and bahn.de. Both will offer the HFC discount. But there is a huge difference in price for date of travel. Tickets bought well in advance can be much cheaper if you choose the non-flexible Super Sparpreis— which is offered by SBB as well as bahn.de.