I'm no expert on bomb wall placement, but I'd say something to avoid is placing them in the middle of long linear stretches of your dungeon. A bomb wall in a dead end is usually the player's fault if they miss it. A bomb wall in a room with two other exits depends on how well it's marked. When the game holds the player's hand for a section and leads them down a linear path, it's very easy to miss a bomb wall branching off from it. I'm also not fond of branch bomb walls before the map is obtainable, unless very little of the dungeon is available to the player from the start. Before you find the map, there's a lot of guesswork invovled and also spacial awareness which not everyone is great with.
Of course given the option between marking and not marking, I'm finding my favorite style is overmarking. This is the thing ALttP does where all the bomb walls are marked but some walls that aren't bombable also have cracks. This narrows down the number of possible bomb spots significantly while also keeping the element of guesswork/logic from Zelda 1.
What I like to do is mark them from a different screen. So, the screen you need to bomb it from you would never know it was a bombable wall.
This can be a cool idea in moderation, but tends to get annoying when used repeatedly, due to all the backtracking. Same goes for hitting a switch that triggers something inaccessible on the current screen so you have to walk around the dungeon to reach it.