I guess that's only for primary items like you point out.
Correct. If a table has an ID field, then deletion can often cause crashes. In a few cases the devs have explicitly fixed this (you CAN delete a Unit, Building, or Technology safely now, as long as you also remember to delete any other table entries involving that unit, like its Flavors or FreePromotions), in others they still haven't (you still can't delete a Promotion without it crashing, unless you immediately fill the now-empty ID slot with a new promotion OR use a utility someone whipped up that renumbers all of the existing promotions to fill in any gaps). These "Primary" tables will also usually have a "Type" field. Not UnitType or BuildingType or whatever, but just a straight Type.
What I refer to as "Secondary" tables are those without ID entries. Secondary tables rarely have default values; the lack of an entry is already treated as a null, effectively, so there's little need for it. These tables will have their identifier entries (unit type, building type, etc.) explicitly link back to a Primary table. You see this in the XML declarations at the top of the file; it'll say that the UnitType field is a Reference pointing back to Units(Type). This is the easy way to distinguish the two types of tables.
The only defaults you'll see in secondaries will be for things like the Unit resource quantity requirement table, where it defaults to using 1 unit of the specified resource but you can change that to 2 or more if you want to (like with the GDR). There are a few other tables that have a few of these, but it's pretty rare.
So again, when you're talking about technologies, it's perfectly safe to delete an entry in the TechPrerequisites table, as long as you make sure you're not left with a tech that has no prerequisites. (If you DO make this mistake, you'll see the tech as researchable from the start.) Actually, that's not quite true; you CAN remove all of a tech's prerequisites and give it the <Disabled> status. It won't be researchable, and will appear on the tech tree in red. You can then use Lua to award that tech if you want, although this causes a bunch of problems with City-States or Barbarians. (Trust me, I've dealt with this more than enough.)