how to build a valid url inside my javascript

Extending my comment as an answer.

Using encodeURIComponent is not only valid and correct, it is actually the only fix for supporting special characters in values in URL which have special meaning for a URL.

Encoding the values in URL component is important for prevent XSS attacks as well. Have a look here

URL-escaping is susceptible to double-escaping, meaning you must URL-escape its parts exactly once. It is best to perform the URL-escaping at the time the URL is being assembled.

However, you can improve your code in the following manner

var inputs = [ "#journal", "#keywords", "#datepub", "#title", "#localcurrency", "#locations", "#dropdown1", "#dropdown2" ];
$(document).ready(function(){
    $('#button').click(function(e) {  
        var count =  1;
        var searchParams = inputs.filter( function( id ){
            return $( "#" + id ).val().trim().length > 0;
        }).map( function( id ){
            var value = encodeURIComponent( $( "#" + id ).val().trim() );
            return "FilterField" + (count) + "=" + id + "&FilterValue" + (count++) + "=" + value;
        }).join( "&" );
        window.location.replace("/teamsites/Bib%20Test/Forms/search.aspx?"+ searchParams );
    });
});

Alternatively, you can also use URL (though not supported in IE)

var inputs = [ "#journal", "#keywords", "#datepub", "#title", "#localcurrency", "#locations", "#dropdown1", "#dropdown2" ];
$(document).ready(function(){
    $('#button').click(function(e) {  
        var count =  1;
        var url = new URL( "/teamsites/Bib%20Test/Forms/search.aspx?", window.location.origin );        
        inputs.forEach( function( id ){
            var value = encodeURIComponent( $( "#" + id ).val().trim() );
            if ( value.length >  0 )
            {
                url.searchParams.append( "FilterField" + count, id );
                url.searchParams.append( "FilterValue" + (count++), value );
            }
        });
        window.location.replace( url.href );
    });
});

As you can see that in this approach as well, you will have to use encodeURIcomponent since as per spec

The append(name, value) method, when invoked, must run these steps:

Append a new name-value pair whose name is name and value is value, to list.

Run the update steps.

there is no guarantee that encoding will be done. So, the explicit encoding necessary!!.

/!\ THIS IS NOT AN ANSWER

In relation with comments

const [
   $("#journal").val(),
   $("#keywords").val(),
   $("#datepub").val(),
   $("#title").val(),
   // ...
].forEach((x) => {
   if (x !== null && x !== '') {
     s += ...;

     count += 1;
   }
});

I use encodeUriComponent for this.

url += "&filter=" + encodeURIComponent(filter);

You want '&' inside the parameter value to be encoded, so you use 'encodeURIComponent' on the value of the parameter, but you don't want to encode the stuff between parameters.

Use this if you are not concerned about Internet Explorer or Edge.

I would recommend to use browser's URL API instead. It is stable and is available in most of the modern browsers to deal with URL specific work natively.

Your code can be changed as follows to use this API. It automatically encodes all the required parameters as per the specs. You don't need to deal with the query parameters manually.

$(document).ready(function() {

  $('#button').click(function(e) {
    var count = 1;
    var s = "";
    var url = new URL("http://yourhost.com/teamsites/Bib%20Test/Forms/search.aspx");

    var inputvalue = $("#journal").val();
    var inputvalue2 = $("#keywords").val();
    var inputvalue3 = $("#datepub").val();
    var inputvalue4 = $("#title").val();
    var inputvalue5 = $("#localcurrency").val();
    var inputvalue6 = $("#locations").val();
    var inputvalue7 = $("#dropdown1").val();
    var inputvalue8 = $("#dropdown2").val();

    if (inputvalue != null && inputvalue != "") {
      url.searchParams.set("FilterField" + count, "Journal");
      url.searchParams.set("FilterValue" + count, inputvalue);
      count++;
    }

    if (inputvalue2 != null && inputvalue2 != "") {
      url.searchParams.set("FilterField" + count, "KeyWords");
      url.searchParams.set("FilterValue" + count, inputvalue2);
      count++;
    }

    if (inputvalue3 != null && inputvalue3 != "") {
      url.searchParams.set("FilterField" + count, "datepub");
      url.searchParams.set("FilterValue" + count, inputvalue3);
      count++;
    }

    if (inputvalue4 != null && inputvalue4 != "") {
      url.searchParams.set("FilterField" + count, "Title");
      url.searchParams.set("FilterValue" + count, inputvalue4);
      count++;
    }

    if (inputvalue5 != null && inputvalue5 != "") {
      url.searchParams.set("FilterField" + count, "localcurrency");
      url.searchParams.set("FilterValue" + count, inputvalue5);
      count++;
    }

    if (inputvalue6 != null && inputvalue6 != "") {
      url.searchParams.set("FilterField" + count, "locations");
      url.searchParams.set("FilterValue" + count, inputvalue6);
      count++;
    }

    if (inputvalue7 != null && inputvalue7 != "") {
      url.searchParams.set("FilterField" + count, "dropdown1");
      url.searchParams.set("FilterValue" + count, inputvalue7);
      count++;
    }

    if (inputvalue8 != null && inputvalue8 != "") {
      url.searchParams.set("FilterField" + count, "dropdown2");
      url.searchParams.set("FilterValue" + count, inputvalue8);
      count++;
    }

    window.location.replace(url.href);

  });
});

In addition to it, I recommend to incorporate the suggestions from @GrégoryNEUT, as it makes the code concise and easy to read.