Generally speaking, yes. Prefectural stations often took the numbers of their network affiliate but they didn’t have to - some chose to stay on the number of their analogue VHF frequency - notably, if that was channel 1, NHK G is found on key 3 instead.
TV Asahi took the opportunity to move to key ID 5 from their previous channel 10, and TV Tokyo the same, moving to key 7 from channel 12. (see response to Moe below for why I’m not saying “LCNs” here.)
As far as I could tell, there’s only two stations left that use key 10, oddly enough one is a Nippon TV affiliate and the other is a TV Tokyo one. The Open Uni of Japan was also another in Tokyo with a high number (it actually used key 12), but it stopped broadcasting terrestrially - moving to satellite-only - in 2018.
Blame that also on Japan aligning the setup with their BS/CS satellite setup (although they have different numbers and such) which predated that and also locked in the 12-key setup. The commercial networks would rather send you to those rather than run multis.
But also, ISDB has limits on how many sub-channels you can run. Technically speaking, it has 13 “segments”, you need 12 to run a HD channel (at least in a Japanese 6 MHz channel… hence “1seg” for the mobile broadcast as that uses the 13th). A 720p service uses 8 segments, an SD service four.
There are stations - like NHK Educational, and certain independents like Tokyo MX - that do run a second channel but they have to reduce their main channel to 720p to do it.
As for LCNs… it’s confusing… there is actually a 3-digit channel number underneath the Japanese remote-key model. So for instance, for NHK ETV - a good example given it’s “remote control ID 2” everywhere - the main feed is channel 021 and the multi-channel is 023 (it used to have 022 but not anymore). The three-digit number would be typable as that’s needed for satellite - in the case of terrestrial, apparently some TVs will also handle the multi-channel by just letting you hit the “2” key again.
In the Japanese model, for someone like NHK E, they technically have all the LCNs in the 02x, 22x, 42x and 62x ranges, but anything above 200 is generally just for separate data feeds and you can’t actually have more than 3 video channels without them all being 1seg or something. 
That LCN system actually allows for 16 networks but given current TVs already had the 12 buttons for satellite and there actually aren’t enough networks on terrestial to fill that, that’s what they’ve gone with.
Worth noting that the way of handling multi-channels is still different to how BS satellite channels do it. Good example of this is private service WOWOW, which has three multi-channels (Prime, Live, Cinema) - to access WOWOW you’d switch to BS and hit the “9” key, but then switching between them is actually done using the colour keys. I understand the way the other BS stations that offer multis do it the same way, using the colour buttons. Then they have their own channel numbers too, which is used more because there are a lot more options than the “blessed” 12 11 channels. It’s an absolute mess.