The wavefunction u(r) is not dimensionless since |u(r)|2 represents a probability per unit length. However, the dimensions of u(r) are not important in this question because u(r) appears on both sides of the Schrödinger equation so that its dimensions automatically cancel out. In other words, you could introduce a dimensionless [itex]\widetilde{u}[/itex](r) such that u(r) = λ[itex]\widetilde{u}[/itex](r) where λ is some constant with dimensions (length)-1/2, but λ would just cancel out when you rewrote the equation in terms of [itex]\widetilde{u}[/itex](r).
As you say, going over to the dimensionless form of the Schrödinger equation still doesn't tell you what the energy levels are. But, it does tell you that if you solved the dimensionless equation for the dimensionless energy levels [itex]\widetilde{E}[/itex], then the energy levels for the original problem would be ##E = (\frac{\hbar^2 k^2}{2m})^{1/3}\widetilde{E}##. That provides some very useful information. For example, if you replace the particle with a different particle with 8 times as much mass, then all of the energy levels would be reduced by 1/2. So you can see how the energy levels scale with the various parameters of the system.