First, I wish to ask how you plan to express your protein. Which type of protein expression method are you going to use? Though this part is somewhat unclear, I assume you are trying to deliver the gene that encodes your protein of interest directly into the hippocampus by virus injection.

If this is the case, then your choice of the cre-line mouse should depend on the cell type you are targeting for the selective expression of your protein in those cells. For example, if you plan to express it in GABAergic cells, you can use GAD2-Cre or VGAT-Cre mice. Or, if your targets are serotonergic cells, you can use SERT-Cre mice. Then, you can conduct stereotactic surgery to inject the virus into the hippocampus with these mice. Consequently, your protein will be expressed specifically in these cell types 2~3 weeks after surgery.

If the Cre recombinases are only expressed in the hippocampus, that is much better for you. But if you are indicating mice with region-specific expression of Cre at the hippocampus globally expressed in all cell types, then it would be challenging to target specific cell types unless your virus can selectively transduce certain cell types.

Of course, it must be noted that all these expression methods rely on Cre-lox recombination. Thus, the virus that encodes your protein sequence must have double-floxed sequences flanking your sequence of interest. This will be indicated as DIO of FLEX in the virus sequence information ("Floxed" means loxP sequences flanking the sequence of interest to be expressed.). If you are not planning to use this type of virus, then there is no point in using cre-line mice.

In addition, based on the second paragraph of your question, I assume you also want to know why there are different strains (ex. different stock no.) of the same cre-line mice. This may depend on the genetic background (ex. congenic or hybrid) or the method of developing such cre-line mice. If this information differs among strains, they would be classified into different stocks even if they have Cre expression at the same cell types. Sometimes, these differences can also determine the rate of unwanted germline recombination of Cre genes during breeding. So if you favor the stable expression of Cre in the course of breeding, you should also consider this issue and choose those with the minimum rate. As far as I know, I don't think there are other criteria for selecting the best model in terms of Cre-lox recombination-mediated gene expression.

The availability and the cost of a specific cre-line mouse model may depend on several factors, such as the model's popularity, fecundity, and the current breeding status at the mouse repository. Costs can also be affected by the overall difficulty of such genetic modifications to generate the cre-line mice. Therefore, you should consider all the abovementioned factors to purchase your mouse model of interest to fulfill your experiment goals.

I hope this helps!