Yes1,
No, replacing deleted 1x1 houses with vacant lots generally does not lead to merging. As VitruviusAIA indicated in reply #1, if a square of four 1x1 houses of the same type doesn't merge (within a few moments), then merging will never occur in that square. (A 2x2 residence can form in that square, of course, but that's something different.) If you didn't understand reply #1 then read it again.
As far as we can tell, the chance of a house merging in a randomly selected 2x2 square is about 62%.
Whether something is a "waste" (of time or money or anything else) depends on what you are trying to accomplish. For example, if the extra consumption of goods of 1x1 houses will eventually become a problem, then not deleting 1x1 houses could be wasteful.
Some of my cities, early ones, have 1x1 houses. (My later cities do not, since nowadays I typically make all houses residences or better.) I don't remember all of the details of the construction of my early cities. In those cities that have sub-residence houses (probably spacious homesteads) that are all 2x2s, I might have made them by deleting the 1x1 houses that wouldn't merge, but I think I tested the map to find some places where 1x1 houses would merge, and then restarted the mission and built the sub-residence houses only in those locations.
There are several ways to form side-by-side residences. The obvious one is to use something solid to block house expansion, like this:
??VVXXVVXXVV??
??VVVVVVVVVV??
RRRRRRRRRRRRRRR
where R=road, V=vacant lot, X=blocking object such as small statue or well. (Naturally, you can start with fewer vacant lots if you want to prevent merging.) When everything needed is supplied, this should become 3 residences and 4 1x1 spacious apartments. Delete the blocking objects and the spacious apartments should form 2 more residences.
To form side-by-side residences without blocking objects, start by putting vacant lots only in places where they must expand correctly. Then after they form residences, add more vacant lots in similar places, and continue the process as long as is necessary. In the above example, you could start with 4 (or 2) vacant lots, 2 (or 1) on each end (touching the question marks). Once those 2 residences form, put in 4 (or 2) more vacant lots, touching the residences. Once those 2 additional residences form, put in the remaining 4 (or 3 or 2 or 1) vacant lots, which will eventually form the final residence.
If you know where houses will merge (either by running a test or by using one of Nero Would's "spoiler" spreadsheets), then there are several other things that you could do. For example, if you know that in a particular 2x6 rectangle, 2x2 sub-residence houses will form in the 3 desired places and will not form in the 2 undesired places, then you could start by placing all 12 vacant lots in that rectangle.